rs12631326

Variant names:

• chr3-144579472-T-C
• rs12631326

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 0.0884 in 152,112 control chromosomes in the GnomAD database, including 739 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 0.088 (739 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.360
• Publications: 1 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 = 0.255 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: 0.0884 AC: 13440 AN: 151994 Hom.: 738 Cov.: 32

Gnomad AFR AF: 0.0728

Gnomad AMI AF: 0.0934

Gnomad AMR AF: 0.0956

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.0475

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0805

Gnomad OTH AF: 0.0982

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

GnomAD4 genome AF: 0.0884 AC: 13449 AN: 152112 Hom.: 739 Cov.: 32 AF XY: 0.0898 AC XY: 6680 AN XY: 74354

African (AFR) AF: 0.0727 AC: 3023 AN: 41556

American (AMR) AF: 0.0955 AC: 1457 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 457 AN: 3466

East Asian (EAS) AF: 0.267 AC: 1376 AN: 5160

South Asian (SAS) AF: 0.176 AC: 849 AN: 4820

European-Finnish (FIN) AF: 0.0475 AC: 505 AN: 10622

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0804 AC: 5462 AN: 67914

Other (OTH) AF: 0.0986 AC: 208 AN: 2110

Alfa AF: 0.0837 Hom.: 597

Bravo AF: 0.0896

Asia WGS AF: 0.237 AC: 821 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.62
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs12631326; hg19: chr3-144298314;