14-105557979-T-C

Variant names:

• chr14-105557979-T-C
• rs4983346

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The variant allele was found at a frequency of 0.101 in 148,820 control chromosomes in the GnomAD database, including 1,985 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 0.10 (1985 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BS2: High Homozygotes in GnomAd4 at 1985 gene

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15022 AN: 148714 Hom.: 1972 Cov.: 32

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0548

Gnomad ASJ AF: 0.0182

Gnomad EAS AF: 0.00170

Gnomad SAS AF: 0.0203

Gnomad FIN AF: 0.0115

Gnomad MID AF: 0.0691

Gnomad NFE AF: 0.0215

Gnomad OTH AF: 0.0820

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

GnomAD4 genome AF: 0.101 AC: 15075 AN: 148820 Hom.: 1985 Cov.: 32 AF XY: 0.0976 AC XY: 7093 AN XY: 72690

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.309 AC: 12312 AN: 39842

American (AMR) AF: 0.0545 AC: 823 AN: 15106

Ashkenazi Jewish (ASJ) AF: 0.0182 AC: 63 AN: 3466

East Asian (EAS) AF: 0.00170 AC: 7 AN: 4108

South Asian (SAS) AF: 0.0208 AC: 98 AN: 4716

European-Finnish (FIN) AF: 0.0115 AC: 122 AN: 10600

Middle Eastern (MID) AF: 0.0775 AC: 22 AN: 284

European-Non Finnish (NFE) AF: 0.0215 AC: 1458 AN: 67748

Other (OTH) AF: 0.0819 AC: 167 AN: 2038

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.0179 Hom.: 37

Bravo AF: 0.120

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.58
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs4983346; hg19: chr14-106024316;