rs625847

Positions:

• chr1-12166660-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0383 in 152,334 control chromosomes in the GnomAD database, including 122 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 0.038 (122 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.560

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0383 (5829/152334) while in subpopulation AFR AF= 0.0456 (1896/41582). AF 95% confidence interval is 0.0439. There are 122 homozygotes in gnomad4. There are 2647 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 122 gene

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: 0.0381 AC: 5804 AN: 152216 Hom.: 117 Cov.: 32

Gnomad AFR AF: 0.0450

Gnomad AMI AF: 0.0462

Gnomad AMR AF: 0.0204

Gnomad ASJ AF: 0.0363

Gnomad EAS AF: 0.0136

Gnomad SAS AF: 0.0238

Gnomad FIN AF: 0.0165

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0444

Gnomad OTH AF: 0.0373

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

GnomAD4 genome AF: 0.0383 AC: 5829 AN: 152334 Hom.: 122 Cov.: 32 AF XY: 0.0355 AC XY: 2647 AN XY: 74494

Gnomad4 AFR AF: 0.0456

Gnomad4 AMR AF: 0.0203

Gnomad4 ASJ AF: 0.0363

Gnomad4 EAS AF: 0.0137

Gnomad4 SAS AF: 0.0236

Gnomad4 FIN AF: 0.0165

Gnomad4 NFE AF: 0.0443

Gnomad4 OTH AF: 0.0365

Alfa AF: 0.0367 Hom.: 14

Bravo AF: 0.0382

Asia WGS AF: 0.0250 AC: 85 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.4
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs625847; hg19: chr1-12226717; COSMIC: COSV66163768;