rs16960843

Variant names:

• chr15-48374628-A-G
• rs16960843

Your query was ambiguous. Multiple possible variants found:

• chr15-48374628-A-G
• chr15-48374628-A-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 0.0602 in 150,294 control chromosomes in the GnomAD database, including 763 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 0.060 (763 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.347 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: 0.0600 AC: 9018 AN: 150180 Hom.: 758 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.00330

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.00696

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.0634

Gnomad FIN AF: 0.0144

Gnomad MID AF: 0.0160

Gnomad NFE AF: 0.00746

Gnomad OTH AF: 0.0559

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

GnomAD4 genome AF: 0.0602 AC: 9053 AN: 150294 Hom.: 763 Cov.: 32 AF XY: 0.0641 AC XY: 4700 AN XY: 73334

African (AFR) AF: 0.104 AC: 4253 AN: 40864

American (AMR) AF: 0.122 AC: 1850 AN: 15136

Ashkenazi Jewish (ASJ) AF: 0.00696 AC: 24 AN: 3448

East Asian (EAS) AF: 0.361 AC: 1847 AN: 5122

South Asian (SAS) AF: 0.0633 AC: 302 AN: 4772

European-Finnish (FIN) AF: 0.0144 AC: 146 AN: 10138

Middle Eastern (MID) AF: 0.0172 AC: 5 AN: 290

European-Non Finnish (NFE) AF: 0.00746 AC: 504 AN: 67536

Other (OTH) AF: 0.0572 AC: 119 AN: 2080

Alfa AF: 0.0366 Hom.: 48

Bravo AF: 0.0742

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.25
DANN	Benign	0.26
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs16960843; hg19: chr15-48666825;