chr13-75043482-G-A

Variant names:

• chr13-75043482-G-A
• rs1340900

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 0.478 in 151,254 control chromosomes in the GnomAD database, including 19,054 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 0.48 (19054 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.640
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.578 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: 0.478 AC: 72270 AN: 151138 Hom.: 19051 Cov.: 30

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.478 AC: 72281 AN: 151254 Hom.: 19054 Cov.: 30 AF XY: 0.477 AC XY: 35249 AN XY: 73884

African (AFR) AF: 0.240 AC: 9904 AN: 41280

American (AMR) AF: 0.546 AC: 8273 AN: 15140

Ashkenazi Jewish (ASJ) AF: 0.555 AC: 1916 AN: 3452

East Asian (EAS) AF: 0.537 AC: 2741 AN: 5100

South Asian (SAS) AF: 0.429 AC: 2062 AN: 4804

European-Finnish (FIN) AF: 0.587 AC: 6174 AN: 10526

Middle Eastern (MID) AF: 0.514 AC: 150 AN: 292

European-Non Finnish (NFE) AF: 0.583 AC: 39430 AN: 67654

Other (OTH) AF: 0.511 AC: 1075 AN: 2104

Alfa AF: 0.506 Hom.: 3544

Bravo AF: 0.468

Asia WGS AF: 0.497 AC: 1727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.0
DANN	Benign	0.63
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs1340900; hg19: chr13-75617619;