rs712442

Variant names:

• chr14-47988144-A-T
• rs712442

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.440

Gnomad4 AMR AF: 0.488

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.650

Gnomad4 SAS AF: 0.525

Gnomad4 FIN AF: 0.516

Gnomad4 NFE AF: 0.425

Gnomad4 OTH AF: 0.397

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs712442; hg19: chr14-48457347;