rs12125971

Variant names:

• chr1-106921021-C-T
• rs12125971

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0692 in 152,252 control chromosomes in the GnomAD database, including 416 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 0.069 (416 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0693 AC: 10539 AN: 152134 Hom.: 417 Cov.: 33

Gnomad AFR AF: 0.0445

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0603

Gnomad ASJ AF: 0.0957

Gnomad EAS AF: 0.0959

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.0523

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0768

Gnomad OTH AF: 0.0847

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

GnomAD4 genome AF: 0.0692 AC: 10543 AN: 152252 Hom.: 416 Cov.: 33 AF XY: 0.0718 AC XY: 5342 AN XY: 74446

African (AFR) AF: 0.0447 AC: 1856 AN: 41552

American (AMR) AF: 0.0602 AC: 920 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0957 AC: 332 AN: 3470

East Asian (EAS) AF: 0.0959 AC: 497 AN: 5180

South Asian (SAS) AF: 0.191 AC: 922 AN: 4828

European-Finnish (FIN) AF: 0.0523 AC: 555 AN: 10612

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0768 AC: 5223 AN: 68000

Other (OTH) AF: 0.0833 AC: 176 AN: 2112

Alfa AF: 0.0743 Hom.: 724

Bravo AF: 0.0653

Asia WGS AF: 0.121 AC: 418 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	19
DANN	Benign	0.79
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs12125971; hg19: chr1-107463643; COSMIC: COSV107159625;