13-74701583-C-T

Variant names:

• chr13-74701583-C-T
• rs2077779

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.598 in 152,020 control chromosomes in the GnomAD database, including 27,521 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 0.60 (27521 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.648

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.598 AC: 90866 AN: 151904 Hom.: 27509 Cov.: 31

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.808

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.659

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

GnomAD4 genome AF: 0.598 AC: 90911 AN: 152020 Hom.: 27521 Cov.: 31 AF XY: 0.601 AC XY: 44648 AN XY: 74306

Gnomad4 AFR AF: 0.566

Gnomad4 AMR AF: 0.629

Gnomad4 ASJ AF: 0.691

Gnomad4 EAS AF: 0.808

Gnomad4 SAS AF: 0.733

Gnomad4 FIN AF: 0.596

Gnomad4 NFE AF: 0.578

Gnomad4 OTH AF: 0.657

Alfa AF: 0.593 Hom.: 13469

Bravo AF: 0.604

Asia WGS AF: 0.745 AC: 2592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.64
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2077779; hg19: chr13-75275720;