rs16952868

Variant names:

• chr15-69154535-C-A
• rs16952868

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 0.468 in 152,032 control chromosomes in the GnomAD database, including 19,569 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 0.47 (19569 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.608 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: 0.469 AC: 71208 AN: 151914 Hom.: 19566 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.468 AC: 71201 AN: 152032 Hom.: 19569 Cov.: 32 AF XY: 0.471 AC XY: 35035 AN XY: 74318

African (AFR) AF: 0.158 AC: 6573 AN: 41488

American (AMR) AF: 0.619 AC: 9453 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.570 AC: 1976 AN: 3468

East Asian (EAS) AF: 0.564 AC: 2909 AN: 5158

South Asian (SAS) AF: 0.485 AC: 2337 AN: 4822

European-Finnish (FIN) AF: 0.574 AC: 6064 AN: 10570

Middle Eastern (MID) AF: 0.528 AC: 153 AN: 290

European-Non Finnish (NFE) AF: 0.591 AC: 40136 AN: 67944

Other (OTH) AF: 0.507 AC: 1070 AN: 2110

Alfa AF: 0.514 Hom.: 3628

Bravo AF: 0.461

Asia WGS AF: 0.459 AC: 1594 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	0.29
DANN	Benign	0.46
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs16952868; hg19: chr15-69446874;