11-13598625-T-C

Position:

• chr11-13598625-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 0.557 in 151,978 control chromosomes in the GnomAD database, including 24,338 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 0.56 (24338 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122

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 (SAS) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84550 AN: 151860 Hom.: 24323 Cov.: 32

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.636

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.557 AC: 84605 AN: 151978 Hom.: 24338 Cov.: 32 AF XY: 0.561 AC XY: 41679 AN XY: 74294

Gnomad4 AFR AF: 0.401

Gnomad4 AMR AF: 0.586

Gnomad4 ASJ AF: 0.706

Gnomad4 EAS AF: 0.534

Gnomad4 SAS AF: 0.637

Gnomad4 FIN AF: 0.626

Gnomad4 NFE AF: 0.622

Gnomad4 OTH AF: 0.566

Alfa AF: 0.614 Hom.: 34591

Bravo AF: 0.541

Asia WGS AF: 0.578 AC: 2011 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	4.7
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9630182; hg19: chr11-13620172;