13-71313177-C-T

Variant names:

• chr13-71313177-C-T
• rs2480555

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 0.829 in 151,690 control chromosomes in the GnomAD database, including 52,278 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 0.83 (52278 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.496
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.869 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: 0.829 AC: 125716 AN: 151572 Hom.: 52251 Cov.: 32

Gnomad AFR AF: 0.761

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.845

Gnomad ASJ AF: 0.838

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.929

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.848

Gnomad OTH AF: 0.820

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

GnomAD4 genome AF: 0.829 AC: 125795 AN: 151690 Hom.: 52278 Cov.: 32 AF XY: 0.833 AC XY: 61785 AN XY: 74180

African (AFR) AF: 0.761 AC: 31538 AN: 41444

American (AMR) AF: 0.845 AC: 12861 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.838 AC: 2903 AN: 3466

East Asian (EAS) AF: 0.891 AC: 4606 AN: 5170

South Asian (SAS) AF: 0.831 AC: 4009 AN: 4822

European-Finnish (FIN) AF: 0.929 AC: 9856 AN: 10610

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.848 AC: 57380 AN: 67644

Other (OTH) AF: 0.818 AC: 1723 AN: 2106

Alfa AF: 0.840 Hom.: 8376

Bravo AF: 0.818

Asia WGS AF: 0.848 AC: 2945 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	13
DANN	Benign	0.59
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs2480555; hg19: chr13-71887309;