11-37179376-G-T

Variant names:

• chr11-37179376-G-T
• rs1461349

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.185 AC: 7676 AN: 41500

American (AMR) AF: 0.391 AC: 5959 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1053 AN: 3472

East Asian (EAS) AF: 0.439 AC: 2257 AN: 5146

South Asian (SAS) AF: 0.285 AC: 1375 AN: 4818

European-Finnish (FIN) AF: 0.522 AC: 5506 AN: 10556

Middle Eastern (MID) AF: 0.250 AC: 73 AN: 292

European-Non Finnish (NFE) AF: 0.393 AC: 26681 AN: 67970

Other (OTH) AF: 0.337 AC: 712 AN: 2112

Alfa AF: 0.377 Hom.: 5728

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
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs1461349; hg19: chr11-37200926;