rs16972208

Variant names:

• chr15-74740246-G-A
• rs16972208

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 0.105 in 152,170 control chromosomes in the GnomAD database, including 1,749 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 0.11 (1749 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.398
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.256 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: 0.105 AC: 15949 AN: 152052 Hom.: 1739 Cov.: 31

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.0317

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.0815

Gnomad FIN AF: 0.0490

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0127

Gnomad OTH AF: 0.0989

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

GnomAD4 genome AF: 0.105 AC: 15993 AN: 152170 Hom.: 1749 Cov.: 31 AF XY: 0.109 AC XY: 8102 AN XY: 74412

African (AFR) AF: 0.202 AC: 8364 AN: 41456

American (AMR) AF: 0.263 AC: 4021 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0317 AC: 110 AN: 3472

East Asian (EAS) AF: 0.266 AC: 1374 AN: 5174

South Asian (SAS) AF: 0.0820 AC: 396 AN: 4828

European-Finnish (FIN) AF: 0.0490 AC: 520 AN: 10618

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0127 AC: 863 AN: 68012

Other (OTH) AF: 0.0979 AC: 207 AN: 2114

Alfa AF: 0.0612 Hom.: 183

Bravo AF: 0.128

Asia WGS AF: 0.185 AC: 641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.5
DANN	Benign	0.74
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs16972208; hg19: chr15-75032587;