Variant chr5-115607014-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001164468.4(TMED7-TICAM2):c.566+9304T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 151,884 control chromosomes in the GnomAD database, including 16,861 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.47 ( 16861 hom., cov: 32)

Consequence

TMED7-TICAM2
NM_001164468.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.70

Variant links:

Genes affected

TMED7-TICAM2 (HGNC:):

TMED7-TICAM2 links:

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

TICAM2-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.03).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Protein
TMED7-TICAM2	NM_001164468.4 linkuse as main transcript	c.566+9304T>C	intron_variant	NP_001157940.1
TICAM2-AS1	NR_109874.1 linkuse as main transcript	n.417+3858A>G	intron_variant, non_coding_transcript_variant
TMED7-TICAM2	NM_001164469.4 linkuse as main transcript	c.566+9304T>C	intron_variant	NP_001157941.1
TICAM2-AS1	NR_109875.1 linkuse as main transcript	n.417+3858A>G	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
TICAM2-AS1	ENST00000668244.1 linkuse as main transcript	n.346+4554A>G	intron_variant, non_coding_transcript_variant
TICAM2-AS1	ENST00000508517.2 linkuse as main transcript	n.455+3858A>G	intron_variant, non_coding_transcript_variant	2
TICAM2-AS1	ENST00000515570.1 linkuse as main transcript	n.112+3858A>G	intron_variant, non_coding_transcript_variant	2

Frequencies

GnomAD3 genomes

AF:

0.469

AC:

71220

AN:

151766

Hom.:

16850

Cov.:

show subpopulations

Gnomad AFR

AF:

0.404

Gnomad AMI

AF:

0.465

Gnomad AMR

AF:

0.426

Gnomad ASJ

AF:

0.521

Gnomad EAS

AF:

0.463

Gnomad SAS

AF:

0.471

Gnomad FIN

AF:

0.525

Gnomad MID

AF:

0.497

Gnomad NFE

AF:

0.508

Gnomad OTH

AF:

0.461

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.469

AC:

71269

AN:

151884

Hom.:

16861

Cov.:

AF XY:

0.470

AC XY:

34928

AN XY:

74260

show subpopulations

Gnomad4 AFR

AF:

0.404

Gnomad4 AMR

AF:

0.426

Gnomad4 ASJ

AF:

0.521

Gnomad4 EAS

AF:

0.462

Gnomad4 SAS

AF:

0.471

Gnomad4 FIN

AF:

0.525

Gnomad4 NFE

AF:

0.508

Gnomad4 OTH

AF:

0.460

Alfa

AF:

0.498

Hom.:

25226

Bravo

AF:

0.455

Asia WGS

AF:

0.407

AC:

1415

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.63

DANN

Benign

0.18

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over