chr1-189908801-G-A

Variant names:

• chr1-189908801-G-A
• rs1341974

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 0.273 in 151,934 control chromosomes in the GnomAD database, including 6,160 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 0.27 (6160 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.379 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: 0.273 AC: 41494 AN: 151818 Hom.: 6150 Cov.: 32

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.273 AC: 41525 AN: 151934 Hom.: 6160 Cov.: 32 AF XY: 0.272 AC XY: 20166 AN XY: 74236

Gnomad4 AFR AF: 0.384

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.298

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.259

Alfa AF: 0.257 Hom.: 1037

Bravo AF: 0.274

Asia WGS AF: 0.232 AC: 798 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.15
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1341974; hg19: chr1-189877931;