rs12123883

Variant names:

• chr1-203195714-T-C
• rs12123883

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.054 in 148,082 control chromosomes in the GnomAD database, including 276 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 0.054 (276 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0761 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: 0.0541 AC: 8002 AN: 147966 Hom.: 276 Cov.: 32

Gnomad AFR AF: 0.0152

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.0533

Gnomad ASJ AF: 0.0612

Gnomad EAS AF: 0.000198

Gnomad SAS AF: 0.0193

Gnomad FIN AF: 0.0780

Gnomad MID AF: 0.0935

Gnomad NFE AF: 0.0779

Gnomad OTH AF: 0.0540

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

GnomAD4 genome AF: 0.0540 AC: 7999 AN: 148082 Hom.: 276 Cov.: 32 AF XY: 0.0537 AC XY: 3879 AN XY: 72302

African (AFR) AF: 0.0152 AC: 584 AN: 38500

American (AMR) AF: 0.0531 AC: 792 AN: 14906

Ashkenazi Jewish (ASJ) AF: 0.0612 AC: 211 AN: 3448

East Asian (EAS) AF: 0.000199 AC: 1 AN: 5030

South Asian (SAS) AF: 0.0193 AC: 92 AN: 4758

European-Finnish (FIN) AF: 0.0780 AC: 821 AN: 10520

Middle Eastern (MID) AF: 0.0944 AC: 27 AN: 286

European-Non Finnish (NFE) AF: 0.0779 AC: 5268 AN: 67664

Other (OTH) AF: 0.0534 AC: 110 AN: 2058

Alfa AF: 0.0603 Hom.: 278

Bravo AF: 0.0502

Asia WGS AF: 0.0110 AC: 38 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.43
DANN	Benign	0.44
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs12123883; hg19: chr1-203164842;