rs11495908

chr4-179783765-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0960

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.0843

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.204

Gnomad4 OTH AF: 0.177

Alfa AF: 0.201 Hom.: 6380

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11495908; hg19: chr4-180704918;