rs12750212

Variant names:

• chr1-209508751-G-A
• rs12750212

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 0.155 in 152,040 control chromosomes in the GnomAD database, including 2,529 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 0.16 (2529 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.295 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: 0.155 AC: 23582 AN: 151922 Hom.: 2521 Cov.: 32

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.0987

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0908

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.155 AC: 23624 AN: 152040 Hom.: 2529 Cov.: 32 AF XY: 0.156 AC XY: 11604 AN XY: 74306

Gnomad4 AFR AF: 0.299

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.0987

Gnomad4 NFE AF: 0.0908

Gnomad4 OTH AF: 0.144

Alfa AF: 0.109 Hom.: 593

Bravo AF: 0.161

Asia WGS AF: 0.162 AC: 562 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.23
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12750212; hg19: chr1-209682096;