rs1444588

Variant names:

• chr12-46070634-C-T
• rs1444588

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 0.475 in 152,108 control chromosomes in the GnomAD database, including 17,343 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 0.47 (17343 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.435
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.487 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: 0.475 AC: 72148 AN: 151990 Hom.: 17326 Cov.: 33

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.475 AC: 72202 AN: 152108 Hom.: 17343 Cov.: 33 AF XY: 0.472 AC XY: 35115 AN XY: 74348

African (AFR) AF: 0.492 AC: 20415 AN: 41478

American (AMR) AF: 0.463 AC: 7077 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1384 AN: 3472

East Asian (EAS) AF: 0.317 AC: 1639 AN: 5168

South Asian (SAS) AF: 0.467 AC: 2257 AN: 4830

European-Finnish (FIN) AF: 0.502 AC: 5310 AN: 10574

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.480 AC: 32618 AN: 67986

Other (OTH) AF: 0.450 AC: 949 AN: 2110

Alfa AF: 0.477 Hom.: 72140

Bravo AF: 0.470

Asia WGS AF: 0.411 AC: 1427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.98
DANN	Benign	0.14
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs1444588; hg19: chr12-46464417;