rs6957003

Variant names:

• chr7-113232951-C-T
• rs6957003
• ENST00000831766.1:n.305-400C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000831766.1(ENSG00000308106):​n.305-400C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0258 in 152,246 control chromosomes in the GnomAD database, including 79 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 0.026 (79 hom., cov: 32)
• Consequence: ENSG00000308106 ENST00000831766.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.215
• Publications: 0 publications found

Genes affected

ENSG00000308106 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0258 (3931/152246) while in subpopulation AFR AF = 0.0444 (1846/41552). AF 95% confidence interval is 0.0427. There are 79 homozygotes in GnomAd4. There are 1924 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 79 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000831766.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308106	ENST00000831766.1		n.305-400C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0258 AC: 3930 AN: 152128 Hom.: 79 Cov.: 32

Gnomad AFR AF: 0.0445

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0155

Gnomad ASJ AF: 0.0524

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0367

Gnomad FIN AF: 0.0110

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0190

Gnomad OTH AF: 0.0277

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

GnomAD4 genome AF: 0.0258 AC: 3931 AN: 152246 Hom.: 79 Cov.: 32 AF XY: 0.0258 AC XY: 1924 AN XY: 74438

African (AFR) AF: 0.0444 AC: 1846 AN: 41552

American (AMR) AF: 0.0154 AC: 236 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0524 AC: 182 AN: 3470

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5186

South Asian (SAS) AF: 0.0367 AC: 177 AN: 4822

European-Finnish (FIN) AF: 0.0110 AC: 117 AN: 10602

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0190 AC: 1292 AN: 68012

Other (OTH) AF: 0.0274 AC: 58 AN: 2116

Alfa AF: 0.0236 Hom.: 8

Bravo AF: 0.0262

Asia WGS AF: 0.0130 AC: 46 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.68
DANN	Benign	0.13
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs6957003; hg19: chr7-112873006;