8-13931799-T-C

Variant names:

• chr8-13931799-T-C
• rs1356946

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 0.038 in 152,216 control chromosomes in the GnomAD database, including 236 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 0.038 (236 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.415
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0380 AC: 5785 AN: 152098 Hom.: 237 Cov.: 31

Gnomad AFR AF: 0.0150

Gnomad AMI AF: 0.0286

Gnomad AMR AF: 0.0247

Gnomad ASJ AF: 0.0519

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.0379

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0360

Gnomad OTH AF: 0.0368

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

GnomAD4 genome AF: 0.0380 AC: 5787 AN: 152216 Hom.: 236 Cov.: 31 AF XY: 0.0399 AC XY: 2973 AN XY: 74420

African (AFR) AF: 0.0151 AC: 627 AN: 41558

American (AMR) AF: 0.0246 AC: 375 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0519 AC: 180 AN: 3468

East Asian (EAS) AF: 0.183 AC: 944 AN: 5156

South Asian (SAS) AF: 0.143 AC: 688 AN: 4824

European-Finnish (FIN) AF: 0.0379 AC: 402 AN: 10616

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0360 AC: 2450 AN: 68014

Other (OTH) AF: 0.0397 AC: 84 AN: 2114

Alfa AF: 0.0344 Hom.: 73

Bravo AF: 0.0337

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.33
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs1356946; hg19: chr8-13789308;