14-47982231-T-C

Variant names:

• chr14-47982231-T-C
• rs712436

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 0.447 in 151,758 control chromosomes in the GnomAD database, including 15,449 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 (15449 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.63 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: 0.447 AC: 67744 AN: 151640 Hom.: 15424 Cov.: 31

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.447 AC: 67821 AN: 151758 Hom.: 15449 Cov.: 31 AF XY: 0.454 AC XY: 33634 AN XY: 74164

African (AFR) AF: 0.424 AC: 17558 AN: 41414

American (AMR) AF: 0.486 AC: 7402 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1421 AN: 3456

East Asian (EAS) AF: 0.648 AC: 3324 AN: 5126

South Asian (SAS) AF: 0.525 AC: 2527 AN: 4812

European-Finnish (FIN) AF: 0.515 AC: 5436 AN: 10548

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.425 AC: 28825 AN: 67870

Other (OTH) AF: 0.390 AC: 820 AN: 2102

Alfa AF: 0.428 Hom.: 43700

Bravo AF: 0.444

Asia WGS AF: 0.546 AC: 1894 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.2
DANN	Benign	0.23
PhyloP100		0.082

Splicing

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

Other links and lift over

dbSNP: rs712436; hg19: chr14-48451434;