1-189862576-A-G

Variant names:

• chr1-189862576-A-G
• rs2944694

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 0.163 in 152,074 control chromosomes in the GnomAD database, including 2,869 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 0.16 (2869 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.322 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: 0.163 AC: 24812 AN: 151956 Hom.: 2863 Cov.: 32

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.0928

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.0701

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.0540

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.163 AC: 24847 AN: 152074 Hom.: 2869 Cov.: 32 AF XY: 0.161 AC XY: 11962 AN XY: 74346

African (AFR) AF: 0.327 AC: 13529 AN: 41426

American (AMR) AF: 0.0926 AC: 1414 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 436 AN: 3468

East Asian (EAS) AF: 0.0704 AC: 364 AN: 5170

South Asian (SAS) AF: 0.228 AC: 1098 AN: 4820

European-Finnish (FIN) AF: 0.0540 AC: 573 AN: 10608

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 6983 AN: 67986

Other (OTH) AF: 0.149 AC: 314 AN: 2114

Alfa AF: 0.134 Hom.: 239

Bravo AF: 0.171

Asia WGS AF: 0.152 AC: 527 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.0
DANN	Benign	0.78
PhyloP100		0.042

Splicing

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

Other links and lift over

dbSNP: rs2944694; hg19: chr1-189831706;