rs964611

Variant names:

• chr15-48305317-C-A
• rs964611

Your query was ambiguous. Multiple possible variants found:

• chr15-48305317-C-A
• chr15-48305317-C-G
• chr15-48305317-C-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 0.141 in 152,164 control chromosomes in the GnomAD database, including 1,601 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 0.14 (1601 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.306

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.173 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: 0.141 AC: 21371 AN: 152046 Hom.: 1596 Cov.: 32

Gnomad AFR AF: 0.0994

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.141 AC: 21394 AN: 152164 Hom.: 1601 Cov.: 32 AF XY: 0.139 AC XY: 10354 AN XY: 74410

Gnomad4 AFR AF: 0.0993

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.179

Alfa AF: 0.154 Hom.: 2538

Bravo AF: 0.142

Asia WGS AF: 0.173 AC: 600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.65
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs964611; hg19: chr15-48597514;