Variant chr5-115616314-T-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

The ENST00000456936.4(TMED7):c.570A>T(p.Ser190=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0165 in 1,614,188 control chromosomes in the GnomAD database, including 289 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.013 ( 19 hom., cov: 33)

Exomes 𝑓: 0.017 ( 270 hom. )

Consequence

TMED7
ENST00000456936.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.235

Variant links:

Genes affected

TMED7 (HGNC:24253): (transmembrane p24 trafficking protein 7) Predicted to be involved in Golgi organization; endoplasmic reticulum to Golgi vesicle-mediated transport; and intracellular protein transport. Located in Golgi apparatus; endoplasmic reticulum; and endoplasmic reticulum-Golgi intermediate compartment. [provided by Alliance of Genome Resources, Apr 2022]

TMED7 links:

TMED7-TICAM2 (HGNC:):

TMED7-TICAM2 links:

TICAM2-AS1 (HGNC:55575): (TICAM2 antisense RNA 1)

TICAM2-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 5-115616314-T-A is Benign according to our data. Variant chr5-115616314-T-A is described in ClinVar as [Benign]. Clinvar id is 1657409.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0127 (1931/152342) while in subpopulation NFE AF= 0.0166 (1132/68018). AF 95% confidence interval is 0.0158. There are 19 homozygotes in gnomad4. There are 920 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 19 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
TMED7	NM_181836.6 linkuse as main transcript	c.570A>T	p.Ser190=	synonymous_variant	3/3	ENST00000456936.4	NP_861974.1
TMED7-TICAM2	NM_001164468.4 linkuse as main transcript	c.566+4A>T		splice_donor_region_variant, intron_variant			NP_001157940.1
TICAM2-AS1	NR_109874.1 linkuse as main transcript	n.418-2825T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMED7	ENST00000456936.4 linkuse as main transcript	c.570A>T	p.Ser190=	synonymous_variant	3/3	1	NM_181836.6	ENSP00000405926	P1	Q9Y3B3-1
TICAM2-AS1	ENST00000668244.1 linkuse as main transcript	n.347-3754T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.0127

AC:

1932

AN:

152224

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00321

Gnomad AMI

AF:

0.0461

Gnomad AMR

AF:

0.0145

Gnomad ASJ

AF:

0.0593

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00414

Gnomad FIN

AF:

0.0104

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.0166

Gnomad OTH

AF:

0.0268

GnomAD3 exomes

AF:

0.0144

AC:

3588

AN:

249374

Hom.:

AF XY:

0.0148

AC XY:

1991

AN XY:

134980

show subpopulations

Gnomad AFR exome

AF:

0.00240

Gnomad AMR exome

AF:

0.00989

Gnomad ASJ exome

AF:

0.0525

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00676

Gnomad FIN exome

AF:

0.0160

Gnomad NFE exome

AF:

0.0179

Gnomad OTH exome

AF:

0.0201

GnomAD4 exome

AF:

0.0169

AC:

24674

AN:

1461846

Hom.:

270

Cov.:

AF XY:

0.0168

AC XY:

12223

AN XY:

727222

show subpopulations

Gnomad4 AFR exome

AF:

0.00275

Gnomad4 AMR exome

AF:

0.0106

Gnomad4 ASJ exome

AF:

0.0524

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00691

Gnomad4 FIN exome

AF:

0.0165

Gnomad4 NFE exome

AF:

0.0180

Gnomad4 OTH exome

AF:

0.0175

GnomAD4 genome

AF:

0.0127

AC:

1931

AN:

152342

Hom.:

Cov.:

AF XY:

0.0123

AC XY:

920

AN XY:

74508

show subpopulations

Gnomad4 AFR

AF:

0.00320

Gnomad4 AMR

AF:

0.0145

Gnomad4 ASJ

AF:

0.0593

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00414

Gnomad4 FIN

AF:

0.0104

Gnomad4 NFE

AF:

0.0166

Gnomad4 OTH

AF:

0.0265

Alfa

AF:

0.0202

Hom.:

Bravo

AF:

0.0134

Asia WGS

AF:

0.00375

AC:

AN:

3478

EpiCase

AF:

0.0192

EpiControl

AF:

0.0184

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 31, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.37

CADD

Benign

7.6

DANN

Benign

0.86

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.58

Details are displayed if max score is > 0.2

DS_DG_spliceai

0.20

Position offset: -42

DS_DL_spliceai

0.58

Position offset: 4

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over