Variant rs7041716 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_032012.4(TMEM245):c.2123+4126G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 511,074 control chromosomes in the GnomAD database, including 4,150 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 0.090 ( 731 hom., cov: 32)

Exomes 𝑓: 0.13 ( 3419 hom. )

Consequence

TMEM245
NM_032012.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.326

Variant links:

Genes affected

TMEM245 (HGNC:1363): (transmembrane protein 245) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

TMEM245 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.73).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TMEM245	NM_032012.4 linkuse as main transcript	c.2123+4126G>T		intron_variant		ENST00000374586.8	NP_114401.2

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris	UniProt
TMEM245	ENST00000374586.8 linkuse as main transcript	c.2123+4126G>T	intron_variant	1	NM_032012.4	ENSP00000363714	P3	Q9H330-2
TMEM245	ENST00000413712.7 linkuse as main transcript	c.2099+4126G>T	intron_variant	2		ENSP00000394798	A1
TMEM245	ENST00000491854.1 linkuse as main transcript	c.*695+4126G>T	intron_variant, NMD_transcript_variant	2		ENSP00000417842

Frequencies

GnomAD3 genomes

AF:

0.0901

AC:

13685

AN:

151940

Hom.:

729

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0391

Gnomad AMI

AF:

0.162

Gnomad AMR

AF:

0.0901

Gnomad ASJ

AF:

0.0979

Gnomad EAS

AF:

0.137

Gnomad SAS

AF:

0.240

Gnomad FIN

AF:

0.0856

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.106

Gnomad OTH

AF:

0.0875

GnomAD4 exome

AF:

0.126

AC:

45248

AN:

359016

Hom.:

3419

AF XY:

0.135

AC XY:

27549

AN XY:

203510

show subpopulations

Gnomad4 AFR exome

AF:

0.0375

Gnomad4 AMR exome

AF:

0.114

Gnomad4 ASJ exome

AF:

0.0985

Gnomad4 EAS exome

AF:

0.141

Gnomad4 SAS exome

AF:

0.228

Gnomad4 FIN exome

AF:

0.0916

Gnomad4 NFE exome

AF:

0.105

Gnomad4 OTH exome

AF:

0.114

GnomAD4 genome

AF:

0.0901

AC:

13698

AN:

152058

Hom.:

731

Cov.:

AF XY:

0.0923

AC XY:

6860

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.0390

Gnomad4 AMR

AF:

0.0906

Gnomad4 ASJ

AF:

0.0979

Gnomad4 EAS

AF:

0.137

Gnomad4 SAS

AF:

0.241

Gnomad4 FIN

AF:

0.0856

Gnomad4 NFE

AF:

0.106

Gnomad4 OTH

AF:

0.0885

Alfa

AF:

0.0472

Hom.:

Bravo

AF:

0.0851

Asia WGS

AF:

0.174

AC:

606

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

6.3

DANN

Benign

0.82

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