rs675302

Variant names:

• chr13-85788633-C-G
• rs675302

Your query was ambiguous. Multiple possible variants found:

• chr13-85788633-C-G
• chr13-85788633-C-T

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 0.267 in 151,684 control chromosomes in the GnomAD database, including 6,247 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 0.27 (6247 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.388
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.613 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: 0.267 AC: 40463 AN: 151566 Hom.: 6235 Cov.: 33

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.267 AC: 40501 AN: 151684 Hom.: 6247 Cov.: 33 AF XY: 0.268 AC XY: 19879 AN XY: 74132

African (AFR) AF: 0.148 AC: 6151 AN: 41440

American (AMR) AF: 0.362 AC: 5505 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1005 AN: 3460

East Asian (EAS) AF: 0.631 AC: 3248 AN: 5150

South Asian (SAS) AF: 0.354 AC: 1706 AN: 4824

European-Finnish (FIN) AF: 0.215 AC: 2270 AN: 10564

Middle Eastern (MID) AF: 0.240 AC: 70 AN: 292

European-Non Finnish (NFE) AF: 0.291 AC: 19724 AN: 67734

Other (OTH) AF: 0.301 AC: 634 AN: 2106

Alfa AF: 0.144 Hom.: 279

Bravo AF: 0.272

Asia WGS AF: 0.464 AC: 1611 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.66
DANN	Benign	0.38
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs675302; hg19: chr13-86362768;