rs11495908

Variant names:

• chr4-179783765-A-G
• rs11495908

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 0.164 in 151,792 control chromosomes in the GnomAD database, including 2,279 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 0.16 (2279 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.201 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: 0.164 AC: 24833 AN: 151674 Hom.: 2282 Cov.: 32

Gnomad AFR AF: 0.0962

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.0841

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.164 AC: 24839 AN: 151792 Hom.: 2279 Cov.: 32 AF XY: 0.162 AC XY: 12029 AN XY: 74184

African (AFR) AF: 0.0960 AC: 3985 AN: 41490

American (AMR) AF: 0.127 AC: 1933 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 870 AN: 3464

East Asian (EAS) AF: 0.0843 AC: 437 AN: 5182

South Asian (SAS) AF: 0.138 AC: 665 AN: 4820

European-Finnish (FIN) AF: 0.224 AC: 2371 AN: 10578

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.204 AC: 13817 AN: 67708

Other (OTH) AF: 0.177 AC: 373 AN: 2106

Alfa AF: 0.194 Hom.: 13284

Bravo AF: 0.155

Asia WGS AF: 0.119 AC: 414 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	6.7
DANN	Benign	0.95
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs11495908; hg19: chr4-180704918;