chr13-71309082-G-A

Variant names:

• chr13-71309082-G-A
• rs9592783

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 0.247 in 152,002 control chromosomes in the GnomAD database, including 5,490 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 0.25 (5490 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0300
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.374 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: 0.247 AC: 37500 AN: 151884 Hom.: 5489 Cov.: 32

Gnomad AFR AF: 0.0892

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.247 AC: 37503 AN: 152002 Hom.: 5490 Cov.: 32 AF XY: 0.253 AC XY: 18793 AN XY: 74310

African (AFR) AF: 0.0891 AC: 3697 AN: 41490

American (AMR) AF: 0.332 AC: 5064 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 810 AN: 3470

East Asian (EAS) AF: 0.168 AC: 868 AN: 5158

South Asian (SAS) AF: 0.389 AC: 1875 AN: 4820

European-Finnish (FIN) AF: 0.368 AC: 3881 AN: 10546

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.303 AC: 20579 AN: 67944

Other (OTH) AF: 0.231 AC: 486 AN: 2108

Alfa AF: 0.289 Hom.: 10441

Bravo AF: 0.233

Asia WGS AF: 0.312 AC: 1085 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.2
DANN	Benign	0.48
PhyloP100		0.030

Splicing

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

Other links and lift over

dbSNP: rs9592783; hg19: chr13-71883214;