13-76930937-G-C

Variant names:

• chr13-76930937-G-C
• rs851251

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 0.238 in 152,094 control chromosomes in the GnomAD database, including 8,177 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 0.24 (8177 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.58 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: 0.238 AC: 36157 AN: 151976 Hom.: 8139 Cov.: 32

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.0905

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.0683

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.238 AC: 36255 AN: 152094 Hom.: 8177 Cov.: 32 AF XY: 0.239 AC XY: 17753 AN XY: 74378

African (AFR) AF: 0.586 AC: 24297 AN: 41428

American (AMR) AF: 0.189 AC: 2883 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 475 AN: 3472

East Asian (EAS) AF: 0.308 AC: 1597 AN: 5178

South Asian (SAS) AF: 0.193 AC: 931 AN: 4822

European-Finnish (FIN) AF: 0.0905 AC: 958 AN: 10590

Middle Eastern (MID) AF: 0.168 AC: 49 AN: 292

European-Non Finnish (NFE) AF: 0.0682 AC: 4641 AN: 68002

Other (OTH) AF: 0.199 AC: 420 AN: 2112

Alfa AF: 0.158 Hom.: 506

Bravo AF: 0.260

Asia WGS AF: 0.279 AC: 972 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.11
DANN	Benign	0.32
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs851251; hg19: chr13-77505071;