rs12141128

Variant names:

• chr1-91908190-A-G
• rs12141128

Your query was ambiguous. Multiple possible variants found:

• chr1-91908190-A-G
• chr1-91908190-A-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.538 in 151,780 control chromosomes in the GnomAD database, including 22,370 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 0.54 (22370 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.62
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.592 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: 0.538 AC: 81644 AN: 151662 Hom.: 22351 Cov.: 31

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.683

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.538 AC: 81700 AN: 151780 Hom.: 22370 Cov.: 31 AF XY: 0.533 AC XY: 39498 AN XY: 74134

African (AFR) AF: 0.495 AC: 20499 AN: 41382

American (AMR) AF: 0.457 AC: 6967 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1713 AN: 3470

East Asian (EAS) AF: 0.386 AC: 1988 AN: 5144

South Asian (SAS) AF: 0.448 AC: 2152 AN: 4808

European-Finnish (FIN) AF: 0.564 AC: 5906 AN: 10474

Middle Eastern (MID) AF: 0.552 AC: 160 AN: 290

European-Non Finnish (NFE) AF: 0.597 AC: 40587 AN: 67970

Other (OTH) AF: 0.527 AC: 1108 AN: 2102

Alfa AF: 0.548 Hom.: 7659

Bravo AF: 0.529

Asia WGS AF: 0.405 AC: 1410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	18
DANN	Benign	0.90
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs12141128; hg19: chr1-92373747;