rs2391406

Variant names:

• chr13-107136524-T-G
• rs2391406

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 0.301 in 152,054 control chromosomes in the GnomAD database, including 7,916 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 0.30 (7916 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.451
• Publications: 4 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 (EAS) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45829 AN: 151936 Hom.: 7918 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.301 AC: 45819 AN: 152054 Hom.: 7916 Cov.: 32 AF XY: 0.300 AC XY: 22327 AN XY: 74316

African (AFR) AF: 0.131 AC: 5442 AN: 41520

American (AMR) AF: 0.361 AC: 5512 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1490 AN: 3464

East Asian (EAS) AF: 0.464 AC: 2387 AN: 5148

South Asian (SAS) AF: 0.289 AC: 1393 AN: 4822

European-Finnish (FIN) AF: 0.326 AC: 3441 AN: 10562

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.366 AC: 24888 AN: 67954

Other (OTH) AF: 0.346 AC: 731 AN: 2110

Alfa AF: 0.350 Hom.: 40470

Bravo AF: 0.297

Asia WGS AF: 0.332 AC: 1156 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.60
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs2391406; hg19: chr13-107788872;