14-83931436-T-C

Variant names:

• chr14-83931436-T-C
• rs7158225

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 0.196 in 152,128 control chromosomes in the GnomAD database, including 3,068 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 0.20 (3068 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.217 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: 0.196 AC: 29855 AN: 152010 Hom.: 3068 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.0982

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.196 AC: 29864 AN: 152128 Hom.: 3068 Cov.: 32 AF XY: 0.198 AC XY: 14700 AN XY: 74390

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.0980

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.195

Gnomad4 OTH AF: 0.173

Alfa AF: 0.180 Hom.: 2481

Bravo AF: 0.191

Asia WGS AF: 0.169 AC: 587 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.5
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7158225; hg19: chr14-84397780;