11-8603448-C-T

Position:

• chr11-8603448-C-T

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 0.602 in 151,784 control chromosomes in the GnomAD database, including 27,841 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 (27841 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.653 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: 0.603 AC: 91384 AN: 151666 Hom.: 27827 Cov.: 31

Gnomad AFR AF: 0.660

Gnomad AMI AF: 0.793

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.602 AC: 91445 AN: 151784 Hom.: 27841 Cov.: 31 AF XY: 0.598 AC XY: 44395 AN XY: 74180

Gnomad4 AFR AF: 0.659

Gnomad4 AMR AF: 0.578

Gnomad4 ASJ AF: 0.477

Gnomad4 EAS AF: 0.464

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.651

Gnomad4 NFE AF: 0.595

Gnomad4 OTH AF: 0.560

Alfa AF: 0.601 Hom.: 10198

Bravo AF: 0.607

Asia WGS AF: 0.430 AC: 1495 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.8
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10743082; hg19: chr11-8624995;