chr13-85652025-G-A

Variant names:

• chr13-85652025-G-A
• rs1764955

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 0.0981 in 151,984 control chromosomes in the GnomAD database, including 1,038 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 0.098 (1038 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.412
• Publications: 1 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 (AMR) allele frequency at 95% confidence interval = 0.219 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: 0.0982 AC: 14911 AN: 151864 Hom.: 1037 Cov.: 32

Gnomad AFR AF: 0.0321

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.0813

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.0572

Gnomad FIN AF: 0.0637

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.0981 AC: 14914 AN: 151984 Hom.: 1038 Cov.: 32 AF XY: 0.0976 AC XY: 7247 AN XY: 74256

African (AFR) AF: 0.0320 AC: 1327 AN: 41456

American (AMR) AF: 0.225 AC: 3439 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0813 AC: 282 AN: 3468

East Asian (EAS) AF: 0.158 AC: 816 AN: 5162

South Asian (SAS) AF: 0.0571 AC: 275 AN: 4820

European-Finnish (FIN) AF: 0.0637 AC: 671 AN: 10540

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7613 AN: 67964

Other (OTH) AF: 0.124 AC: 261 AN: 2110

Alfa AF: 0.110 Hom.: 597

Bravo AF: 0.108

Asia WGS AF: 0.0900 AC: 313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.3
DANN	Benign	0.95
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs1764955; hg19: chr13-86226160;