chr15-32700910-C-T

Variant names:

• chr15-32700910-C-T
• rs16969681

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.0698

Gnomad4 EAS AF: 0.379

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.0892

Gnomad4 NFE AF: 0.0860

Gnomad4 OTH AF: 0.119

Alfa AF: 0.0966 Hom.: 603

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16969681; hg19: chr15-32993111;