rs712442

chr14-47988144-A-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;