rs2689132

Variant names:

• chr1-238768952-A-G
• rs2689132

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 0.12 in 152,172 control chromosomes in the GnomAD database, including 1,693 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 0.12 (1693 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.499

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.254 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: 0.119 AC: 18168 AN: 152054 Hom.: 1695 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0934

Gnomad EAS AF: 0.0339

Gnomad SAS AF: 0.0740

Gnomad FIN AF: 0.0402

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0632

Gnomad OTH AF: 0.0926

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

GnomAD4 genome AF: 0.120 AC: 18192 AN: 152172 Hom.: 1693 Cov.: 32 AF XY: 0.118 AC XY: 8752 AN XY: 74406

Gnomad4 AFR AF: 0.258

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.0934

Gnomad4 EAS AF: 0.0340

Gnomad4 SAS AF: 0.0740

Gnomad4 FIN AF: 0.0402

Gnomad4 NFE AF: 0.0632

Gnomad4 OTH AF: 0.0917

Alfa AF: 0.0888 Hom.: 320

Bravo AF: 0.131

Asia WGS AF: 0.0670 AC: 233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.044
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2689132; hg19: chr1-238932252;