rs12049351

Variant names:

• chr1-229582254-C-G
• rs12049351

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 0.233 in 152,078 control chromosomes in the GnomAD database, including 4,350 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 0.23 (4350 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• 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: 0.233 AC: 35438 AN: 151960 Hom.: 4330 Cov.: 32

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.233 AC: 35489 AN: 152078 Hom.: 4350 Cov.: 32 AF XY: 0.231 AC XY: 17162 AN XY: 74350

African (AFR) AF: 0.299 AC: 12409 AN: 41470

American (AMR) AF: 0.251 AC: 3830 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 1167 AN: 3470

East Asian (EAS) AF: 0.166 AC: 858 AN: 5154

South Asian (SAS) AF: 0.182 AC: 873 AN: 4808

European-Finnish (FIN) AF: 0.143 AC: 1514 AN: 10584

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 13992 AN: 67996

Other (OTH) AF: 0.253 AC: 535 AN: 2112

Alfa AF: 0.220 Hom.: 442

Bravo AF: 0.246

Asia WGS AF: 0.188 AC: 655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.37
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs12049351; hg19: chr1-229718001;