rs4945087

Variant names:

• chr11-76425438-G-A
• rs4945087

Your query was ambiguous. Multiple possible variants found:

• chr11-76425438-G-A
• chr11-76425438-G-T

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 0.399 in 152,010 control chromosomes in the GnomAD database, including 12,499 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 0.40 (12499 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.493 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: 0.399 AC: 60591 AN: 151890 Hom.: 12482 Cov.: 32

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.399 AC: 60630 AN: 152010 Hom.: 12499 Cov.: 32 AF XY: 0.400 AC XY: 29726 AN XY: 74292

African (AFR) AF: 0.317 AC: 13125 AN: 41456

American (AMR) AF: 0.483 AC: 7383 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1103 AN: 3472

East Asian (EAS) AF: 0.385 AC: 1993 AN: 5176

South Asian (SAS) AF: 0.509 AC: 2449 AN: 4808

European-Finnish (FIN) AF: 0.388 AC: 4097 AN: 10554

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.430 AC: 29197 AN: 67956

Other (OTH) AF: 0.397 AC: 839 AN: 2112

Alfa AF: 0.424 Hom.: 59369

Bravo AF: 0.399

Asia WGS AF: 0.434 AC: 1510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.1
DANN	Benign	0.54
PhyloP100		-0.068

Splicing

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

Other links and lift over

dbSNP: rs4945087; hg19: chr11-76136482;