chr13-64371042-C-G

Variant names:

• chr13-64371042-C-G
• rs9598783

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 0.43 in 151,908 control chromosomes in the GnomAD database, including 14,456 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 0.43 (14456 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.513 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: 0.430 AC: 65211 AN: 151790 Hom.: 14430 Cov.: 31

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.430 AC: 65291 AN: 151908 Hom.: 14456 Cov.: 31 AF XY: 0.425 AC XY: 31548 AN XY: 74218

African (AFR) AF: 0.414 AC: 17125 AN: 41412

American (AMR) AF: 0.523 AC: 7970 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1427 AN: 3472

East Asian (EAS) AF: 0.237 AC: 1213 AN: 5126

South Asian (SAS) AF: 0.390 AC: 1879 AN: 4812

European-Finnish (FIN) AF: 0.307 AC: 3246 AN: 10572

Middle Eastern (MID) AF: 0.346 AC: 101 AN: 292

European-Non Finnish (NFE) AF: 0.455 AC: 30918 AN: 67952

Other (OTH) AF: 0.436 AC: 918 AN: 2106

Alfa AF: 0.451 Hom.: 1961

Bravo AF: 0.445

Asia WGS AF: 0.372 AC: 1293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.38
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs9598783; hg19: chr13-64945174;