chr1-238745053-C-G

Variant names:

• chr1-238745053-C-G
• rs2689154

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 0.339 in 151,830 control chromosomes in the GnomAD database, including 9,006 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 0.34 (9006 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.210

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.368 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: 0.339 AC: 51416 AN: 151712 Hom.: 8999 Cov.: 31

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.339 AC: 51438 AN: 151830 Hom.: 9006 Cov.: 31 AF XY: 0.336 AC XY: 24920 AN XY: 74198

Gnomad4 AFR AF: 0.336

Gnomad4 AMR AF: 0.237

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.180

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.432

Gnomad4 NFE AF: 0.371

Gnomad4 OTH AF: 0.322

Alfa AF: 0.249 Hom.: 618

Bravo AF: 0.326

Asia WGS AF: 0.177 AC: 619 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.2
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2689154; hg19: chr1-238908353;