rs645925

Variant names:

• chr1-232360556-G-A
• rs645925

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 0.409 in 151,902 control chromosomes in the GnomAD database, including 13,189 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 0.41 (13189 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.618

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.479 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: 0.409 AC: 62090 AN: 151784 Hom.: 13184 Cov.: 31

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.409 AC: 62117 AN: 151902 Hom.: 13189 Cov.: 31 AF XY: 0.401 AC XY: 29751 AN XY: 74244

Gnomad4 AFR AF: 0.340

Gnomad4 AMR AF: 0.372

Gnomad4 ASJ AF: 0.429

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.427

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.483

Gnomad4 OTH AF: 0.424

Alfa AF: 0.463 Hom.: 9865

Bravo AF: 0.403

Asia WGS AF: 0.303 AC: 1061 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.6
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs645925; hg19: chr1-232496302; COSMIC: COSV60038952;