14-82363875-C-T

Variant names:

• chr14-82363875-C-T
• rs10483957

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 0.485 in 151,060 control chromosomes in the GnomAD database, including 18,434 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 0.48 (18434 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.628 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: 0.485 AC: 73192 AN: 150942 Hom.: 18440 Cov.: 29

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.783

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.485 AC: 73205 AN: 151060 Hom.: 18434 Cov.: 29 AF XY: 0.489 AC XY: 36095 AN XY: 73768

African (AFR) AF: 0.375 AC: 15401 AN: 41094

American (AMR) AF: 0.467 AC: 7059 AN: 15130

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2087 AN: 3470

East Asian (EAS) AF: 0.367 AC: 1877 AN: 5120

South Asian (SAS) AF: 0.647 AC: 3078 AN: 4758

European-Finnish (FIN) AF: 0.570 AC: 5959 AN: 10454

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.529 AC: 35863 AN: 67754

Other (OTH) AF: 0.491 AC: 1021 AN: 2080

Alfa AF: 0.517 Hom.: 86504

Bravo AF: 0.470

Asia WGS AF: 0.463 AC: 1611 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	8.5
DANN	Benign	0.75
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs10483957; hg19: chr14-82830219;