rs6957496

Variant names:

• chr7-136867090-A-G
• rs6957496
• ENST00000439694.5:n.344-81199T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000439694.5(ENSG00000234352):​n.344-81199T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 152,178 control chromosomes in the GnomAD database, including 1,702 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 0.13 (1702 hom., cov: 32)
• Consequence: ENSG00000234352 ENST00000439694.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07

Genes affected

ENSG00000234352 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234352	ENST00000439694.5	n.344-81199T>C		intron_variant	Intron 3 of 3	1
ENSG00000234352	ENST00000586239.5	n.274-81199T>C		intron_variant	Intron 2 of 4	5
ENSG00000234352	ENST00000592183.5	n.475-81199T>C		intron_variant	Intron 3 of 3	4

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19180 AN: 152060 Hom.: 1697 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.0787

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.0720

Gnomad FIN AF: 0.0446

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0937

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.126 AC: 19212 AN: 152178 Hom.: 1702 Cov.: 32 AF XY: 0.121 AC XY: 9028 AN XY: 74414

Gnomad4 AFR AF: 0.240

Gnomad4 AMR AF: 0.0786

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.000964

Gnomad4 SAS AF: 0.0733

Gnomad4 FIN AF: 0.0446

Gnomad4 NFE AF: 0.0937

Gnomad4 OTH AF: 0.107

Alfa AF: 0.101 Hom.: 462

Bravo AF: 0.134

Asia WGS AF: 0.0430 AC: 151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.024
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6957496; hg19: chr7-136551837;