chr13-73244591-T-A

Variant names:

• chr13-73244591-T-A
• rs9530176

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 0.259 in 152,140 control chromosomes in the GnomAD database, including 6,672 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 0.26 (6672 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.781
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.377 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: 0.259 AC: 39337 AN: 152022 Hom.: 6670 Cov.: 32

Gnomad AFR AF: 0.0664

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.259 AC: 39332 AN: 152140 Hom.: 6672 Cov.: 32 AF XY: 0.254 AC XY: 18912 AN XY: 74378

African (AFR) AF: 0.0662 AC: 2749 AN: 41554

American (AMR) AF: 0.239 AC: 3653 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1078 AN: 3470

East Asian (EAS) AF: 0.00271 AC: 14 AN: 5174

South Asian (SAS) AF: 0.167 AC: 806 AN: 4822

European-Finnish (FIN) AF: 0.397 AC: 4192 AN: 10558

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.381 AC: 25879 AN: 67968

Other (OTH) AF: 0.270 AC: 572 AN: 2116

Alfa AF: 0.317 Hom.: 1082

Bravo AF: 0.239

Asia WGS AF: 0.0840 AC: 294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.6
DANN	Benign	0.69
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs9530176; hg19: chr13-73818728;