rs870114

chr12-42757501-C-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 0.103 in 152,154 control chromosomes in the GnomAD database, including 869 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 0.10 (869 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.214 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: 0.103 AC: 15683 AN: 152036 Hom.: 868 Cov.: 32

Gnomad AFR AF: 0.0952

Gnomad AMI AF: 0.0418

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0895

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.103 AC: 15700 AN: 152154 Hom.: 869 Cov.: 32 AF XY: 0.107 AC XY: 7967 AN XY: 74382

Gnomad4 AFR AF: 0.0953

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.178

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.0896

Gnomad4 OTH AF: 0.105

Alfa AF: 0.0938 Hom.: 975

Bravo AF: 0.0985

Asia WGS AF: 0.178 AC: 616 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
Cadd	Benign	13
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs870114; hg19: chr12-43151303;