chr14-104659175-G-A

Position:

• chr14-104659175-G-A

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 0.203 in 152,092 control chromosomes in the GnomAD database, including 3,697 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 (3697 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30924 AN: 151974 Hom.: 3694 Cov.: 32

Gnomad AFR AF: 0.0874

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.0491

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.203 AC: 30930 AN: 152092 Hom.: 3697 Cov.: 32 AF XY: 0.202 AC XY: 15050 AN XY: 74338

Gnomad4 AFR AF: 0.0872

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.272

Gnomad4 EAS AF: 0.0491

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.230

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.243

Alfa AF: 0.112 Hom.: 193

Bravo AF: 0.199

Asia WGS AF: 0.139 AC: 482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.8
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4075355; hg19: chr14-105125512;