rs73531535

chr16-20093716-C-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 0.165 in 146,588 control chromosomes in the GnomAD database, including 2,169 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 0.16 (2169 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.988

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.241 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: 0.165 AC: 24111 AN: 146490 Hom.: 2173 Cov.: 29

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.0508

Gnomad AMR AF: 0.0906

Gnomad ASJ AF: 0.0844

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.0826

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.0662

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.165 AC: 24121 AN: 146588 Hom.: 2169 Cov.: 29 AF XY: 0.165 AC XY: 11727 AN XY: 70960

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.0905

Gnomad4 ASJ AF: 0.0844

Gnomad4 EAS AF: 0.252

Gnomad4 SAS AF: 0.0813

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.136

Gnomad4 OTH AF: 0.123

Alfa AF: 0.158 Hom.: 234

Bravo AF: 0.155

Asia WGS AF: 0.151 AC: 524 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	7.0
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs73531535; hg19: chr16-20105038;