rs9592783

Positions:

• chr13-71309082-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0891

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.233

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.389

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.231

Alfa AF: 0.288 Hom.: 7537

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9592783; hg19: chr13-71883214;