rs665808

Variant names:

• chr13-48911777-T-C
• rs665808

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 0.495 in 151,882 control chromosomes in the GnomAD database, including 20,900 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 0.49 (20900 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.331

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.619 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: 0.495 AC: 75155 AN: 151764 Hom.: 20907 Cov.: 31

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.495 AC: 75161 AN: 151882 Hom.: 20900 Cov.: 31 AF XY: 0.498 AC XY: 36965 AN XY: 74238

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.535

Gnomad4 ASJ AF: 0.598

Gnomad4 EAS AF: 0.389

Gnomad4 SAS AF: 0.564

Gnomad4 FIN AF: 0.613

Gnomad4 NFE AF: 0.624

Gnomad4 OTH AF: 0.514

Alfa AF: 0.589 Hom.: 12299

Bravo AF: 0.474

Asia WGS AF: 0.450 AC: 1560 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.9
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs665808; hg19: chr13-49485913; COSMIC: COSV56526730;