rs4478959

Variant names:

• chr11-101023695-A-G
• rs4478959

Your query was ambiguous. Multiple possible variants found:

• chr11-101023695-A-G
• chr11-101023695-A-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 0.224 in 151,972 control chromosomes in the GnomAD database, including 5,027 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 0.22 (5027 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0670
• Publications: 0 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 = 0.701 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: 0.224 AC: 34043 AN: 151854 Hom.: 5014 Cov.: 32

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.0892

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.224 AC: 34096 AN: 151972 Hom.: 5027 Cov.: 32 AF XY: 0.232 AC XY: 17211 AN XY: 74284

African (AFR) AF: 0.299 AC: 12372 AN: 41422

American (AMR) AF: 0.246 AC: 3764 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 474 AN: 3470

East Asian (EAS) AF: 0.720 AC: 3732 AN: 5182

South Asian (SAS) AF: 0.373 AC: 1801 AN: 4824

European-Finnish (FIN) AF: 0.205 AC: 2154 AN: 10532

Middle Eastern (MID) AF: 0.0890 AC: 26 AN: 292

European-Non Finnish (NFE) AF: 0.136 AC: 9211 AN: 67956

Other (OTH) AF: 0.199 AC: 421 AN: 2112

Alfa AF: 0.177 Hom.: 494

Bravo AF: 0.231

Asia WGS AF: 0.532 AC: 1823 AN: 3434

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.69
PhyloP100		-0.067

Splicing

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

Other links and lift over

dbSNP: rs4478959; hg19: chr11-100894426;