rs7304057

Positions:

• chr12-130868017-A-G
• chr12-130868017-A-T

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 0.137 in 151,984 control chromosomes in the GnomAD database, including 1,443 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 0.14 (1443 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.46

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.14 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: 0.137 AC: 20771 AN: 151866 Hom.: 1437 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.0973

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.118

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.137 AC: 20793 AN: 151984 Hom.: 1443 Cov.: 32 AF XY: 0.136 AC XY: 10079 AN XY: 74290

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.0974

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.143

Gnomad4 OTH AF: 0.134

Alfa AF: 0.132 Hom.: 173

Bravo AF: 0.133

Asia WGS AF: 0.118 AC: 409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.0
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7304057; hg19: chr12-131352562;