rs712442

Variant names:

• chr14-47988144-A-T
• rs712442

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 0.452 in 152,026 control chromosomes in the GnomAD database, including 15,845 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 0.45 (15845 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.704
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.631 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: 0.452 AC: 68616 AN: 151906 Hom.: 15813 Cov.: 33

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.648

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.452 AC: 68701 AN: 152026 Hom.: 15845 Cov.: 33 AF XY: 0.458 AC XY: 34050 AN XY: 74298

African (AFR) AF: 0.440 AC: 18265 AN: 41476

American (AMR) AF: 0.488 AC: 7441 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1427 AN: 3470

East Asian (EAS) AF: 0.650 AC: 3358 AN: 5170

South Asian (SAS) AF: 0.525 AC: 2530 AN: 4822

European-Finnish (FIN) AF: 0.516 AC: 5451 AN: 10568

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.425 AC: 28884 AN: 67950

Other (OTH) AF: 0.397 AC: 838 AN: 2112

Alfa AF: 0.454 Hom.: 1927

Bravo AF: 0.449

Asia WGS AF: 0.546 AC: 1892 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.39
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs712442; hg19: chr14-48457347;