chr16-75213493-A-G

Variant names:

• chr16-75213493-A-G
• rs7202844

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 0.137 in 152,152 control chromosomes in the GnomAD database, including 1,646 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 0.14 (1646 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.274
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20792 AN: 152034 Hom.: 1639 Cov.: 33

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0763

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.0802

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.0732

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.137 AC: 20820 AN: 152152 Hom.: 1646 Cov.: 33 AF XY: 0.136 AC XY: 10137 AN XY: 74390

African (AFR) AF: 0.209 AC: 8665 AN: 41494

American (AMR) AF: 0.107 AC: 1637 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0763 AC: 265 AN: 3472

East Asian (EAS) AF: 0.203 AC: 1044 AN: 5154

South Asian (SAS) AF: 0.0786 AC: 379 AN: 4820

European-Finnish (FIN) AF: 0.139 AC: 1474 AN: 10584

Middle Eastern (MID) AF: 0.0685 AC: 20 AN: 292

European-Non Finnish (NFE) AF: 0.102 AC: 6943 AN: 68012

Other (OTH) AF: 0.132 AC: 280 AN: 2114

Alfa AF: 0.121 Hom.: 177

Bravo AF: 0.139

Asia WGS AF: 0.157 AC: 548 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.20
DANN	Benign	0.54
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs7202844; hg19: chr16-75247391;