11-17652683-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 0.566 in 152,008 control chromosomes in the GnomAD database, including 27,457 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 0.57 (27457 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.985

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.881 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: 0.566 AC: 85981 AN: 151890 Hom.: 27463 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.745

Gnomad EAS AF: 0.903

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.566 AC: 85988 AN: 152008 Hom.: 27457 Cov.: 32 AF XY: 0.570 AC XY: 42358 AN XY: 74294

Gnomad4 AFR AF: 0.253

Gnomad4 AMR AF: 0.640

Gnomad4 ASJ AF: 0.745

Gnomad4 EAS AF: 0.903

Gnomad4 SAS AF: 0.573

Gnomad4 FIN AF: 0.718

Gnomad4 NFE AF: 0.678

Gnomad4 OTH AF: 0.602

Alfa AF: 0.627 Hom.: 5081

Bravo AF: 0.552

Asia WGS AF: 0.696 AC: 2415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
Cadd	Benign	16
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3935159; hg19: chr11-17674230;