rs16970854

Variant names:

• chr15-40593429-A-T
• rs16970854

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 0.0836 in 151,962 control chromosomes in the GnomAD database, including 540 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 0.084 (540 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.886

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 = 0.112 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: 0.0836 AC: 12690 AN: 151844 Hom.: 535 Cov.: 33

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.0595

Gnomad AMR AF: 0.0624

Gnomad ASJ AF: 0.0375

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0770

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0687

Gnomad OTH AF: 0.0770

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

GnomAD4 genome AF: 0.0836 AC: 12704 AN: 151962 Hom.: 540 Cov.: 33 AF XY: 0.0838 AC XY: 6224 AN XY: 74280

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.0625

Gnomad4 ASJ AF: 0.0375

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.0770

Gnomad4 NFE AF: 0.0687

Gnomad4 OTH AF: 0.0772

Alfa AF: 0.0859 Hom.: 64

Bravo AF: 0.0842

Asia WGS AF: 0.102 AC: 354 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.0
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16970854; hg19: chr15-40885627;