rs16960540

Variant names:

• chr15-48077377-C-T
• rs16960540

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 0.0383 in 152,326 control chromosomes in the GnomAD database, including 307 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 0.038 (307 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.526
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.269 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: 0.0382 AC: 5819 AN: 152208 Hom.: 308 Cov.: 32

Gnomad AFR AF: 0.0210

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0734

Gnomad ASJ AF: 0.00749

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.0441

Gnomad FIN AF: 0.0220

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0261

Gnomad OTH AF: 0.0439

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

GnomAD4 genome AF: 0.0383 AC: 5827 AN: 152326 Hom.: 307 Cov.: 32 AF XY: 0.0404 AC XY: 3010 AN XY: 74478

African (AFR) AF: 0.0211 AC: 876 AN: 41576

American (AMR) AF: 0.0736 AC: 1126 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.00749 AC: 26 AN: 3472

East Asian (EAS) AF: 0.281 AC: 1450 AN: 5164

South Asian (SAS) AF: 0.0443 AC: 214 AN: 4828

European-Finnish (FIN) AF: 0.0220 AC: 234 AN: 10626

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0261 AC: 1779 AN: 68032

Other (OTH) AF: 0.0444 AC: 94 AN: 2116

Alfa AF: 0.0285 Hom.: 23

Bravo AF: 0.0454

Asia WGS AF: 0.150 AC: 520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.4
DANN	Benign	0.55
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs16960540; hg19: chr15-48369574;