rs1564981

Variant names:

• chr16-50952397-G-A
• rs1564981

Your query was ambiguous. Multiple possible variants found:

• chr16-50952397-G-A
• chr16-50952397-G-C
• chr16-50952397-G-T

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 0.6 in 152,100 control chromosomes in the GnomAD database, including 29,888 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 0.60 (29888 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.854 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: 0.600 AC: 91139 AN: 151982 Hom.: 29831 Cov.: 32

Gnomad AFR AF: 0.861

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.693

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.594

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

GnomAD4 genome AF: 0.600 AC: 91252 AN: 152100 Hom.: 29888 Cov.: 32 AF XY: 0.604 AC XY: 44868 AN XY: 74328

Gnomad4 AFR AF: 0.862

Gnomad4 AMR AF: 0.602

Gnomad4 ASJ AF: 0.647

Gnomad4 EAS AF: 0.692

Gnomad4 SAS AF: 0.741

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.598

Alfa AF: 0.493 Hom.: 31523

Bravo AF: 0.625

Asia WGS AF: 0.726 AC: 2527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.27
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1564981; hg19: chr16-50986308;