rs1019531

chr16-76157639-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;