chr11-13598625-T-C

Variant names:

• chr11-13598625-T-C
• rs9630182

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;