14-47982231-T-C

Variant names:

• chr14-47982231-T-C
• rs712436

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 0.447 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.424

Gnomad4 AMR AF: 0.486

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.648

Gnomad4 SAS AF: 0.525

Gnomad4 FIN AF: 0.515

Gnomad4 NFE AF: 0.425

Gnomad4 OTH AF: 0.390

Alfa AF: 0.423 Hom.: 27585

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs712436; hg19: chr14-48451434;