13-111036888-A-G

Variant names:

• chr13-111036888-A-G
• rs885339

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 0.748 in 152,162 control chromosomes in the GnomAD database, including 43,520 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 0.75 (43520 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.323
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.816 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: 0.748 AC: 113763 AN: 152042 Hom.: 43482 Cov.: 32

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.919

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.793

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.864

Gnomad MID AF: 0.688

Gnomad NFE AF: 0.822

Gnomad OTH AF: 0.757

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

GnomAD4 genome AF: 0.748 AC: 113859 AN: 152162 Hom.: 43520 Cov.: 32 AF XY: 0.749 AC XY: 55741 AN XY: 74408

African (AFR) AF: 0.593 AC: 24591 AN: 41490

American (AMR) AF: 0.740 AC: 11311 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.749 AC: 2598 AN: 3468

East Asian (EAS) AF: 0.793 AC: 4107 AN: 5176

South Asian (SAS) AF: 0.744 AC: 3582 AN: 4816

European-Finnish (FIN) AF: 0.864 AC: 9163 AN: 10608

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.822 AC: 55870 AN: 68002

Other (OTH) AF: 0.758 AC: 1600 AN: 2110

Alfa AF: 0.785 Hom.: 57064

Bravo AF: 0.732

Asia WGS AF: 0.770 AC: 2679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.76
DANN	Benign	0.38
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs885339; hg19: chr13-111689235;