rs510319

Variant names:

• chr7-126163907-C-T
• rs510319

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.347 in 151,652 control chromosomes in the GnomAD database, including 12,832 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 0.35 (12832 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.700
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52513 AN: 151534 Hom.: 12785 Cov.: 32

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.347 AC: 52603 AN: 151652 Hom.: 12832 Cov.: 32 AF XY: 0.348 AC XY: 25792 AN XY: 74164

African (AFR) AF: 0.701 AC: 29003 AN: 41402

American (AMR) AF: 0.239 AC: 3642 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 450 AN: 3462

East Asian (EAS) AF: 0.312 AC: 1608 AN: 5154

South Asian (SAS) AF: 0.235 AC: 1129 AN: 4814

European-Finnish (FIN) AF: 0.324 AC: 3423 AN: 10554

Middle Eastern (MID) AF: 0.182 AC: 53 AN: 292

European-Non Finnish (NFE) AF: 0.185 AC: 12527 AN: 67734

Other (OTH) AF: 0.281 AC: 592 AN: 2108

Alfa AF: 0.231 Hom.: 14647

Bravo AF: 0.356

Asia WGS AF: 0.273 AC: 947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.98
DANN	Benign	0.44
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs510319; hg19: chr7-125803961;