11-37179376-G-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 0.339 in 152,020 control chromosomes in the GnomAD database, including 9,629 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 0.34 (9629 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.332

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 (EAS) allele frequency at 95% confidence interval = 0.424 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: 0.339 AC: 51523 AN: 151902 Hom.: 9625 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.339 AC: 51540 AN: 152020 Hom.: 9629 Cov.: 32 AF XY: 0.344 AC XY: 25550 AN XY: 74262

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.439

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.522

Gnomad4 NFE AF: 0.393

Gnomad4 OTH AF: 0.337

Alfa AF: 0.377 Hom.: 5142

Bravo AF: 0.325

Asia WGS AF: 0.350 AC: 1214 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.98
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1461349; hg19: chr11-37200926;