13-68440680-G-A

Variant names:

• chr13-68440680-G-A
• rs966715

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 0.112 in 149,272 control chromosomes in the GnomAD database, including 1,040 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 0.11 (1040 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.834
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.112 AC: 16689 AN: 149188 Hom.: 1039 Cov.: 31

Gnomad AFR AF: 0.0729

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.0776

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.112 AC: 16708 AN: 149272 Hom.: 1040 Cov.: 31 AF XY: 0.114 AC XY: 8303 AN XY: 72678

African (AFR) AF: 0.0732 AC: 2985 AN: 40776

American (AMR) AF: 0.182 AC: 2716 AN: 14958

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 666 AN: 3462

East Asian (EAS) AF: 0.159 AC: 804 AN: 5046

South Asian (SAS) AF: 0.172 AC: 814 AN: 4740

European-Finnish (FIN) AF: 0.0776 AC: 756 AN: 9748

Middle Eastern (MID) AF: 0.213 AC: 61 AN: 286

European-Non Finnish (NFE) AF: 0.110 AC: 7417 AN: 67276

Other (OTH) AF: 0.133 AC: 277 AN: 2076

Alfa AF: 0.116 Hom.: 605

Bravo AF: 0.118

Asia WGS AF: 0.176 AC: 607 AN: 3440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.75
DANN	Benign	0.45
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs966715; hg19: chr13-69014812;