rs2944694

chr1-189862576-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 0.163 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.327

Gnomad4 AMR AF: 0.0926

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.0704

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.0540

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.149

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2944694; hg19: chr1-189831706;