rs12741825

Positions:

• chr1-159700355-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 0.237 in 152,152 control chromosomes in the GnomAD database, including 5,296 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 0.24 (5296 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.361

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.31 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: 0.237 AC: 36051 AN: 152034 Hom.: 5295 Cov.: 32

Gnomad AFR AF: 0.0717

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.0610

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.237 AC: 36068 AN: 152152 Hom.: 5296 Cov.: 32 AF XY: 0.240 AC XY: 17818 AN XY: 74384

Gnomad4 AFR AF: 0.0715

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.0609

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.348

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.254

Alfa AF: 0.253 Hom.: 830

Bravo AF: 0.229

Asia WGS AF: 0.161 AC: 563 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.7
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12741825; hg19: chr1-159670145;