rs12154270

Positions:

• chr7-84714942-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.148 in 152,008 control chromosomes in the GnomAD database, including 2,013 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 0.15 (2013 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.670

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.211 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: 0.148 AC: 22496 AN: 151890 Hom.: 2015 Cov.: 31

Gnomad AFR AF: 0.0564

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.0672

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.148 AC: 22494 AN: 152008 Hom.: 2013 Cov.: 31 AF XY: 0.146 AC XY: 10820 AN XY: 74282

Gnomad4 AFR AF: 0.0564

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.0673

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.162

Alfa AF: 0.200 Hom.: 4137

Bravo AF: 0.140

Asia WGS AF: 0.0950 AC: 330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	17
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12154270; hg19: chr7-84344258;