1-189761918-A-G

Variant names:

• chr1-189761918-A-G
• rs12132519

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 0.453 in 151,970 control chromosomes in the GnomAD database, including 15,864 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 0.45 (15864 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.443

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.471 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: 0.453 AC: 68836 AN: 151852 Hom.: 15857 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.453 AC: 68868 AN: 151970 Hom.: 15864 Cov.: 32 AF XY: 0.450 AC XY: 33427 AN XY: 74258

Gnomad4 AFR AF: 0.446

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.445

Gnomad4 EAS AF: 0.410

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.524

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.422

Alfa AF: 0.463 Hom.: 7699

Bravo AF: 0.442

Asia WGS AF: 0.401 AC: 1400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.6
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12132519; hg19: chr1-189731048; COSMIC: COSV60003618;