rs7324250

Positions:

• chr13-111516530-A-C
• chr13-111516530-A-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 0.719 in 152,112 control chromosomes in the GnomAD database, including 39,511 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 0.72 (39511 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

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 (EAS) allele frequency at 95% confidence interval = 0.831 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.719 AC: 109260 AN: 151994 Hom.: 39465 Cov.: 33

Gnomad AFR AF: 0.670

Gnomad AMI AF: 0.697

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.852

Gnomad SAS AF: 0.726

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.719 AC: 109370 AN: 152112 Hom.: 39511 Cov.: 33 AF XY: 0.721 AC XY: 53623 AN XY: 74360

Gnomad4 AFR AF: 0.670

Gnomad4 AMR AF: 0.713

Gnomad4 ASJ AF: 0.667

Gnomad4 EAS AF: 0.852

Gnomad4 SAS AF: 0.725

Gnomad4 FIN AF: 0.775

Gnomad4 NFE AF: 0.735

Gnomad4 OTH AF: 0.693

Alfa AF: 0.725 Hom.: 61150

Bravo AF: 0.712

Asia WGS AF: 0.783 AC: 2723 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	1.1
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7324250; hg19: chr13-112168877;