chr13-56860460-G-C

Variant names:

• chr13-56860460-G-C
• rs7333137

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.305 in 151,844 control chromosomes in the GnomAD database, including 8,312 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 0.31 (8312 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.200
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.44 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: 0.305 AC: 46309 AN: 151726 Hom.: 8304 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.305 AC: 46320 AN: 151844 Hom.: 8312 Cov.: 32 AF XY: 0.306 AC XY: 22737 AN XY: 74194

African (AFR) AF: 0.120 AC: 4983 AN: 41494

American (AMR) AF: 0.449 AC: 6821 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.473 AC: 1641 AN: 3466

East Asian (EAS) AF: 0.252 AC: 1301 AN: 5158

South Asian (SAS) AF: 0.303 AC: 1459 AN: 4818

European-Finnish (FIN) AF: 0.365 AC: 3856 AN: 10570

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.370 AC: 25116 AN: 67828

Other (OTH) AF: 0.346 AC: 727 AN: 2102

Alfa AF: 0.319 Hom.: 1074

Bravo AF: 0.307

Asia WGS AF: 0.257 AC: 895 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	15
DANN	Benign	0.68
PhyloP100		0.20

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7333137;

hg19: chr13-57434594;