11-2172945-T-C

Position:

• chr11-2172945-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 0.881 in 152,216 control chromosomes in the GnomAD database, including 59,060 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 0.88 (59060 hom., cov: 33)
  • Exomes 𝑓: 0.89 (917 hom.)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.937 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: 0.881 AC: 133999 AN: 152098 Hom.: 59021 Cov.: 33

Gnomad AFR AF: 0.851

Gnomad AMI AF: 0.965

Gnomad AMR AF: 0.916

Gnomad ASJ AF: 0.881

Gnomad EAS AF: 0.959

Gnomad SAS AF: 0.957

Gnomad FIN AF: 0.883

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.879

Gnomad OTH AF: 0.863

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.893 AC: 2053 AN: 2298 Hom.: 917 AF XY: 0.888 AC XY: 1032 AN XY: 1162

Gnomad4 AFR exome AF: 0.808

Gnomad4 AMR exome AF: 0.875

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.968

Gnomad4 FIN exome AF: 0.800

Gnomad4 NFE exome AF: 0.902

Gnomad4 OTH exome AF: 0.891

GnomAD4 genome AF: 0.881 AC: 134092 AN: 152216 Hom.: 59060 Cov.: 33 AF XY: 0.884 AC XY: 65734 AN XY: 74400

Gnomad4 AFR AF: 0.851

Gnomad4 AMR AF: 0.916

Gnomad4 ASJ AF: 0.881

Gnomad4 EAS AF: 0.959

Gnomad4 SAS AF: 0.957

Gnomad4 FIN AF: 0.883

Gnomad4 NFE AF: 0.879

Gnomad4 OTH AF: 0.864

Alfa AF: 0.879 Hom.: 18663

Bravo AF: 0.879

Asia WGS AF: 0.962 AC: 3346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.0
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10743149; hg19: chr11-2194175;