11-38481061-T-C

Variant names:

• chr11-38481061-T-C
• rs11034770

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 0.338 in 152,004 control chromosomes in the GnomAD database, including 11,406 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 (11406 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.39
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.498 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: 0.338 AC: 51353 AN: 151886 Hom.: 11407 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.0215

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.338 AC: 51339 AN: 152004 Hom.: 11406 Cov.: 32 AF XY: 0.331 AC XY: 24618 AN XY: 74282

African (AFR) AF: 0.0999 AC: 4144 AN: 41502

American (AMR) AF: 0.270 AC: 4120 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1351 AN: 3470

East Asian (EAS) AF: 0.0215 AC: 111 AN: 5154

South Asian (SAS) AF: 0.219 AC: 1054 AN: 4822

European-Finnish (FIN) AF: 0.485 AC: 5105 AN: 10522

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.502 AC: 34133 AN: 67944

Other (OTH) AF: 0.330 AC: 696 AN: 2112

Alfa AF: 0.392 Hom.: 2383

Bravo AF: 0.310

Asia WGS AF: 0.110 AC: 383 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.56
DANN	Benign	0.69
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs11034770; hg19: chr11-38502611;