rs677332

Variant names:

• chr13-33069767-A-G
• rs677332

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 0.34 in 152,140 control chromosomes in the GnomAD database, including 9,890 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 0.34 (9890 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.888
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51689 AN: 152022 Hom.: 9874 Cov.: 33

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.340 AC: 51727 AN: 152140 Hom.: 9890 Cov.: 33 AF XY: 0.339 AC XY: 25209 AN XY: 74386

African (AFR) AF: 0.177 AC: 7353 AN: 41516

American (AMR) AF: 0.477 AC: 7282 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1559 AN: 3466

East Asian (EAS) AF: 0.154 AC: 800 AN: 5188

South Asian (SAS) AF: 0.314 AC: 1515 AN: 4818

European-Finnish (FIN) AF: 0.385 AC: 4074 AN: 10580

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.410 AC: 27840 AN: 67978

Other (OTH) AF: 0.378 AC: 799 AN: 2112

Alfa AF: 0.385 Hom.: 23674

Bravo AF: 0.344

Asia WGS AF: 0.274 AC: 956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.1
DANN	Benign	0.73
PhyloP100		0.89

Splicing

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

Other links and lift over

dbSNP: rs677332; hg19: chr13-33643904;