rs73531535

Variant names:

• chr16-20093716-C-T
• rs73531535

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.234 AC: 9353 AN: 39912

American (AMR) AF: 0.0905 AC: 1249 AN: 13800

Ashkenazi Jewish (ASJ) AF: 0.0844 AC: 290 AN: 3434

East Asian (EAS) AF: 0.252 AC: 1215 AN: 4812

South Asian (SAS) AF: 0.0813 AC: 366 AN: 4500

European-Finnish (FIN) AF: 0.225 AC: 2187 AN: 9710

Middle Eastern (MID) AF: 0.0787 AC: 20 AN: 254

European-Non Finnish (NFE) AF: 0.136 AC: 9148 AN: 67244

Other (OTH) AF: 0.123 AC: 247 AN: 2016

Alfa AF: 0.160 Hom.: 247

Bravo AF: 0.155

Asia WGS AF: 0.151 AC: 524 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.0
DANN	Benign	0.79
PhyloP100		0.99

Splicing

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

Other links and lift over

dbSNP: rs73531535; hg19: chr16-20105038;