rs652625

chr1-12165294-T-Achr1-12165294-T-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 0.131 in 152,110 control chromosomes in the GnomAD database, including 2,345 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 0.13 (2345 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.478

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.315 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: 0.130 AC: 19827 AN: 151992 Hom.: 2329 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.0614

Gnomad ASJ AF: 0.0444

Gnomad EAS AF: 0.0139

Gnomad SAS AF: 0.0332

Gnomad FIN AF: 0.0532

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0648

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.131 AC: 19902 AN: 152110 Hom.: 2345 Cov.: 32 AF XY: 0.125 AC XY: 9293 AN XY: 74358

Gnomad4 AFR AF: 0.320

Gnomad4 AMR AF: 0.0612

Gnomad4 ASJ AF: 0.0444

Gnomad4 EAS AF: 0.0139

Gnomad4 SAS AF: 0.0324

Gnomad4 FIN AF: 0.0532

Gnomad4 NFE AF: 0.0648

Gnomad4 OTH AF: 0.120

Alfa AF: 0.0956 Hom.: 160

Bravo AF: 0.139

Asia WGS AF: 0.0560 AC: 195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.48
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs652625; hg19: chr1-12225351; COSMIC: COSV66163762;