chr14-83806111-T-C

Variant names:

• chr14-83806111-T-C
• rs10484108

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 0.0785 in 152,088 control chromosomes in the GnomAD database, including 1,312 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 0.078 (1312 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.807
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.245 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: 0.0784 AC: 11915 AN: 151970 Hom.: 1312 Cov.: 32

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0324

Gnomad ASJ AF: 0.0127

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0184

Gnomad FIN AF: 0.00330

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0119

Gnomad OTH AF: 0.0600

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

GnomAD4 genome AF: 0.0785 AC: 11932 AN: 152088 Hom.: 1312 Cov.: 32 AF XY: 0.0760 AC XY: 5654 AN XY: 74356

African (AFR) AF: 0.249 AC: 10316 AN: 41476

American (AMR) AF: 0.0324 AC: 495 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0127 AC: 44 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5174

South Asian (SAS) AF: 0.0178 AC: 86 AN: 4824

European-Finnish (FIN) AF: 0.00330 AC: 35 AN: 10604

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0119 AC: 811 AN: 67948

Other (OTH) AF: 0.0594 AC: 125 AN: 2106

Alfa AF: 0.0303 Hom.: 112

Bravo AF: 0.0889

Asia WGS AF: 0.0180 AC: 62 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	3.2
DANN	Benign	0.57
PhyloP100		0.81

Splicing

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

Other links and lift over

dbSNP: rs10484108; hg19: chr14-84272455;