13-106749020-G-C

Variant names:

• chr13-106749020-G-C
• rs2391376

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 0.597 in 151,980 control chromosomes in the GnomAD database, including 28,256 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 0.60 (28256 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.692 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: 0.597 AC: 90638 AN: 151862 Hom.: 28244 Cov.: 31

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.597 AC: 90687 AN: 151980 Hom.: 28256 Cov.: 31 AF XY: 0.604 AC XY: 44878 AN XY: 74278

African (AFR) AF: 0.415 AC: 17166 AN: 41410

American (AMR) AF: 0.652 AC: 9945 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.680 AC: 2361 AN: 3472

East Asian (EAS) AF: 0.496 AC: 2553 AN: 5150

South Asian (SAS) AF: 0.712 AC: 3428 AN: 4816

European-Finnish (FIN) AF: 0.760 AC: 8036 AN: 10580

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.663 AC: 45098 AN: 67972

Other (OTH) AF: 0.594 AC: 1255 AN: 2114

Alfa AF: 0.548 Hom.: 1783

Bravo AF: 0.579

Asia WGS AF: 0.614 AC: 2133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.011
DANN	Benign	0.48
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2391376; hg19: chr13-107401368;