chr13-72273956-G-A

Variant names:

• chr13-72273956-G-A
• rs340560

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 0.106 in 126,802 control chromosomes in the GnomAD database, including 1,582 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 0.11 (1582 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.2 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: 0.106 AC: 13386 AN: 126716 Hom.: 1573 Cov.: 24

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.0440

Gnomad AMR AF: 0.0747

Gnomad ASJ AF: 0.0798

Gnomad EAS AF: 0.0586

Gnomad SAS AF: 0.0434

Gnomad FIN AF: 0.0197

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0745

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.106 AC: 13411 AN: 126802 Hom.: 1582 Cov.: 24 AF XY: 0.102 AC XY: 6303 AN XY: 61802

African (AFR) AF: 0.204 AC: 7198 AN: 35270

American (AMR) AF: 0.0746 AC: 958 AN: 12842

Ashkenazi Jewish (ASJ) AF: 0.0798 AC: 225 AN: 2820

East Asian (EAS) AF: 0.0590 AC: 247 AN: 4188

South Asian (SAS) AF: 0.0432 AC: 174 AN: 4024

European-Finnish (FIN) AF: 0.0197 AC: 172 AN: 8728

Middle Eastern (MID) AF: 0.143 AC: 30 AN: 210

European-Non Finnish (NFE) AF: 0.0746 AC: 4188 AN: 56176

Other (OTH) AF: 0.105 AC: 184 AN: 1748

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.0
DANN	Benign	0.89
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs340560; hg19: chr13-72848094;