rs1347851

Variant names:

• chr12-90173201-C-T
• rs1347851

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 0.807 in 151,934 control chromosomes in the GnomAD database, including 49,708 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 0.81 (49708 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.859 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: 0.808 AC: 122593 AN: 151816 Hom.: 49669 Cov.: 31

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.793

Gnomad AMR AF: 0.735

Gnomad ASJ AF: 0.813

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.780

Gnomad OTH AF: 0.796

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

GnomAD4 genome AF: 0.807 AC: 122684 AN: 151934 Hom.: 49708 Cov.: 31 AF XY: 0.810 AC XY: 60138 AN XY: 74252

African (AFR) AF: 0.867 AC: 35936 AN: 41472

American (AMR) AF: 0.734 AC: 11184 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.813 AC: 2820 AN: 3470

East Asian (EAS) AF: 0.879 AC: 4513 AN: 5132

South Asian (SAS) AF: 0.820 AC: 3956 AN: 4822

European-Finnish (FIN) AF: 0.823 AC: 8717 AN: 10598

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.780 AC: 52943 AN: 67886

Other (OTH) AF: 0.793 AC: 1674 AN: 2112

Alfa AF: 0.793 Hom.: 34472

Bravo AF: 0.802

Asia WGS AF: 0.810 AC: 2818 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.066
DANN	Benign	0.23
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1347851; hg19: chr12-90566978;