rs16960538

Variant names:

• chr15-48077288-A-G
• rs16960538

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 0.0444 in 152,284 control chromosomes in the GnomAD database, including 341 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 0.044 (341 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.00
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.269 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: 0.0443 AC: 6746 AN: 152166 Hom.: 342 Cov.: 32

Gnomad AFR AF: 0.0231

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0773

Gnomad ASJ AF: 0.00922

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.0441

Gnomad FIN AF: 0.0318

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0357

Gnomad OTH AF: 0.0493

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

GnomAD4 genome AF: 0.0444 AC: 6754 AN: 152284 Hom.: 341 Cov.: 32 AF XY: 0.0465 AC XY: 3462 AN XY: 74452

African (AFR) AF: 0.0232 AC: 966 AN: 41572

American (AMR) AF: 0.0775 AC: 1186 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.00922 AC: 32 AN: 3470

East Asian (EAS) AF: 0.281 AC: 1453 AN: 5166

South Asian (SAS) AF: 0.0444 AC: 214 AN: 4822

European-Finnish (FIN) AF: 0.0318 AC: 338 AN: 10620

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0357 AC: 2431 AN: 68014

Other (OTH) AF: 0.0497 AC: 105 AN: 2112

Alfa AF: 0.0360 Hom.: 16

Bravo AF: 0.0509

Asia WGS AF: 0.151 AC: 523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.6
DANN	Benign	0.58
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs16960538; hg19: chr15-48369485;