rs16961323

Variant names:

• chr15-48666885-G-A
• rs16961323

Your query was ambiguous. Multiple possible variants found:

• chr15-48666885-G-A
• chr15-48666885-G-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 0.0706 in 152,272 control chromosomes in the GnomAD database, including 694 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 0.071 (694 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.841
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0706 AC: 10740 AN: 152154 Hom.: 693 Cov.: 32

Gnomad AFR AF: 0.0183

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.0570

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0810

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0604

Gnomad OTH AF: 0.0905

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

GnomAD4 genome AF: 0.0706 AC: 10749 AN: 152272 Hom.: 694 Cov.: 32 AF XY: 0.0748 AC XY: 5573 AN XY: 74464

African (AFR) AF: 0.0183 AC: 759 AN: 41560

American (AMR) AF: 0.175 AC: 2679 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0570 AC: 198 AN: 3472

East Asian (EAS) AF: 0.258 AC: 1335 AN: 5176

South Asian (SAS) AF: 0.115 AC: 553 AN: 4824

European-Finnish (FIN) AF: 0.0810 AC: 860 AN: 10614

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0604 AC: 4109 AN: 68028

Other (OTH) AF: 0.0976 AC: 206 AN: 2110

Alfa AF: 0.0690 Hom.: 1024

Bravo AF: 0.0793

Asia WGS AF: 0.195 AC: 676 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.16
DANN	Benign	0.76
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs16961323; hg19: chr15-48959082;