rs9572182

Positions:

• chr13-69512198-T-C
• chr13-69512198-T-G

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 0.475 in 152,028 control chromosomes in the GnomAD database, including 17,378 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 0.47 (17378 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.706

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.512 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: 0.474 AC: 72068 AN: 151910 Hom.: 17355 Cov.: 32

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.465

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

GnomAD4 genome AF: 0.475 AC: 72140 AN: 152028 Hom.: 17378 Cov.: 32 AF XY: 0.474 AC XY: 35263 AN XY: 74320

Gnomad4 AFR AF: 0.433

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.433

Gnomad4 SAS AF: 0.462

Gnomad4 FIN AF: 0.480

Gnomad4 NFE AF: 0.517

Gnomad4 OTH AF: 0.466

Alfa AF: 0.496 Hom.: 30902

Bravo AF: 0.466

Asia WGS AF: 0.421 AC: 1465 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9572182; hg19: chr13-70086330;