rs12123383

Variant names:

• chr1-19060091-A-C
• rs12123383

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 0.258 in 143,152 control chromosomes in the GnomAD database, including 5,058 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 0.26 (5058 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0900
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.421 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: 0.258 AC: 36917 AN: 143046 Hom.: 5051 Cov.: 25

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.258 AC: 36944 AN: 143152 Hom.: 5058 Cov.: 25 AF XY: 0.264 AC XY: 18330 AN XY: 69542

African (AFR) AF: 0.241 AC: 9385 AN: 38968

American (AMR) AF: 0.224 AC: 3210 AN: 14344

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1021 AN: 3358

East Asian (EAS) AF: 0.299 AC: 1455 AN: 4870

South Asian (SAS) AF: 0.437 AC: 1903 AN: 4352

European-Finnish (FIN) AF: 0.295 AC: 2848 AN: 9656

Middle Eastern (MID) AF: 0.418 AC: 118 AN: 282

European-Non Finnish (NFE) AF: 0.251 AC: 16191 AN: 64492

Other (OTH) AF: 0.278 AC: 550 AN: 1976

Alfa AF: 0.260 Hom.: 7044

Bravo AF: 0.261

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.30
PhyloP100		0.090

Splicing

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

Other links and lift over

dbSNP: rs12123383; hg19: chr1-19386585;