rs2689132

Positions:

• chr1-238768952-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 0.12 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;