rs11918665

Positions:

• chr3-186495995-A-G
• chr3-186495995-A-T

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 0.904 in 152,330 control chromosomes in the GnomAD database, including 62,374 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 0.90 (62374 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.158

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.965 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.904 AC: 137533 AN: 152212 Hom.: 62317 Cov.: 33

Gnomad AFR AF: 0.972

Gnomad AMI AF: 0.930

Gnomad AMR AF: 0.898

Gnomad ASJ AF: 0.866

Gnomad EAS AF: 0.947

Gnomad SAS AF: 0.863

Gnomad FIN AF: 0.884

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.867

Gnomad OTH AF: 0.895

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

GnomAD4 genome AF: 0.904 AC: 137649 AN: 152330 Hom.: 62374 Cov.: 33 AF XY: 0.905 AC XY: 67383 AN XY: 74470

Gnomad4 AFR AF: 0.973

Gnomad4 AMR AF: 0.898

Gnomad4 ASJ AF: 0.866

Gnomad4 EAS AF: 0.946

Gnomad4 SAS AF: 0.863

Gnomad4 FIN AF: 0.884

Gnomad4 NFE AF: 0.867

Gnomad4 OTH AF: 0.895

Alfa AF: 0.874 Hom.: 73820

Bravo AF: 0.910

Asia WGS AF: 0.920 AC: 3201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.5
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11918665; hg19: chr3-186213784;