rs1019531

Variant names:

• chr16-76157639-T-C
• rs1019531

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 0.0715 in 152,136 control chromosomes in the GnomAD database, including 851 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 0.071 (851 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.191 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: 0.0713 AC: 10844 AN: 152018 Hom.: 849 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0257

Gnomad ASJ AF: 0.00749

Gnomad EAS AF: 0.0998

Gnomad SAS AF: 0.0867

Gnomad FIN AF: 0.0201

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0162

Gnomad OTH AF: 0.0507

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

GnomAD4 genome AF: 0.0715 AC: 10872 AN: 152136 Hom.: 851 Cov.: 32 AF XY: 0.0712 AC XY: 5298 AN XY: 74390

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.0257

Gnomad4 ASJ AF: 0.00749

Gnomad4 EAS AF: 0.0994

Gnomad4 SAS AF: 0.0865

Gnomad4 FIN AF: 0.0201

Gnomad4 NFE AF: 0.0162

Gnomad4 OTH AF: 0.0516

Alfa AF: 0.0247 Hom.: 305

Bravo AF: 0.0757

Asia WGS AF: 0.0990 AC: 343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.52
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1019531; hg19: chr16-76191537;