1-189761918-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;