chr13-74640391-G-A

Variant names:

• chr13-74640391-G-A
• rs10507828

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 0.241 in 152,072 control chromosomes in the GnomAD database, including 4,526 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 0.24 (4526 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.273 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: 0.241 AC: 36634 AN: 151954 Hom.: 4526 Cov.: 33

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.241 AC: 36642 AN: 152072 Hom.: 4526 Cov.: 33 AF XY: 0.236 AC XY: 17560 AN XY: 74336

African (AFR) AF: 0.193 AC: 8019 AN: 41512

American (AMR) AF: 0.216 AC: 3308 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1105 AN: 3472

East Asian (EAS) AF: 0.268 AC: 1388 AN: 5180

South Asian (SAS) AF: 0.196 AC: 946 AN: 4820

European-Finnish (FIN) AF: 0.196 AC: 2064 AN: 10554

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18736 AN: 67930

Other (OTH) AF: 0.280 AC: 591 AN: 2112

Alfa AF: 0.272 Hom.: 22844

Bravo AF: 0.244

Asia WGS AF: 0.218 AC: 757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.6
DANN	Benign	0.42
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs10507828; hg19: chr13-75214528;