chr13-48911777-T-C

Position:

• chr13-48911777-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;