rs16969681

Variant names:

• chr15-32700910-C-T
• rs16969681

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 0.118 in 152,088 control chromosomes in the GnomAD database, including 1,308 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 0.12 (1308 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 51 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.365 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: 0.118 AC: 17955 AN: 151970 Hom.: 1305 Cov.: 33

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.0698

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.0892

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0860

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.118 AC: 17965 AN: 152088 Hom.: 1308 Cov.: 33 AF XY: 0.122 AC XY: 9068 AN XY: 74328

African (AFR) AF: 0.128 AC: 5300 AN: 41484

American (AMR) AF: 0.143 AC: 2180 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0698 AC: 242 AN: 3468

East Asian (EAS) AF: 0.379 AC: 1957 AN: 5160

South Asian (SAS) AF: 0.234 AC: 1127 AN: 4822

European-Finnish (FIN) AF: 0.0892 AC: 942 AN: 10566

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0860 AC: 5847 AN: 68000

Other (OTH) AF: 0.119 AC: 250 AN: 2108

Alfa AF: 0.101 Hom.: 2499

Bravo AF: 0.123

Asia WGS AF: 0.300 AC: 1038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.49
DANN	Benign	0.80
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs16969681; hg19: chr15-32993111;