13-82123686-T-C

Variant names:

• chr13-82123686-T-C
• rs1331584

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 0.926 in 152,174 control chromosomes in the GnomAD database, including 65,416 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 0.93 (65416 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.973 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: 0.926 AC: 140823 AN: 152056 Hom.: 65347 Cov.: 32

Gnomad AFR AF: 0.981

Gnomad AMI AF: 0.819

Gnomad AMR AF: 0.936

Gnomad ASJ AF: 0.876

Gnomad EAS AF: 0.954

Gnomad SAS AF: 0.894

Gnomad FIN AF: 0.921

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.896

Gnomad OTH AF: 0.911

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

GnomAD4 genome AF: 0.926 AC: 140952 AN: 152174 Hom.: 65416 Cov.: 32 AF XY: 0.927 AC XY: 68942 AN XY: 74400

African (AFR) AF: 0.981 AC: 40757 AN: 41544

American (AMR) AF: 0.936 AC: 14310 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.876 AC: 3038 AN: 3470

East Asian (EAS) AF: 0.954 AC: 4940 AN: 5176

South Asian (SAS) AF: 0.893 AC: 4282 AN: 4794

European-Finnish (FIN) AF: 0.921 AC: 9757 AN: 10594

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.896 AC: 60937 AN: 67990

Other (OTH) AF: 0.912 AC: 1927 AN: 2114

Alfa AF: 0.934 Hom.: 24532

Bravo AF: 0.931

Asia WGS AF: 0.938 AC: 3246 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.24
DANN	Benign	0.50
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1331584; hg19: chr13-82697821;