rs13242133

chr7-1249643-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 0.684 in 148,758 control chromosomes in the GnomAD database, including 36,489 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 0.68 (36489 hom., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.814 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: 0.684 AC: 101649 AN: 148640 Hom.: 36481 Cov.: 22

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.606

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.773

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.836

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.792

Gnomad OTH AF: 0.698

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

GnomAD4 genome AF: 0.684 AC: 101687 AN: 148758 Hom.: 36489 Cov.: 22 AF XY: 0.685 AC XY: 49615 AN XY: 72400

Gnomad4 AFR AF: 0.459

Gnomad4 AMR AF: 0.668

Gnomad4 ASJ AF: 0.773

Gnomad4 EAS AF: 0.706

Gnomad4 SAS AF: 0.836

Gnomad4 FIN AF: 0.772

Gnomad4 NFE AF: 0.792

Gnomad4 OTH AF: 0.700

Alfa AF: 0.768 Hom.: 38649

Bravo AF: 0.662

Asia WGS AF: 0.777 AC: 2700 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	2.7
Dann	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13242133; hg19: chr7-1289279;