14-101295704-C-G

Position:

• chr14-101295704-C-G

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 0.227 in 152,236 control chromosomes in the GnomAD database, including 4,193 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 0.23 (4193 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.295 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: 0.227 AC: 34542 AN: 152118 Hom.: 4181 Cov.: 33

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.227 AC: 34596 AN: 152236 Hom.: 4193 Cov.: 33 AF XY: 0.231 AC XY: 17188 AN XY: 74446

Gnomad4 AFR AF: 0.299

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.304

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.196

Alfa AF: 0.0967 Hom.: 140

Bravo AF: 0.224

Asia WGS AF: 0.182 AC: 633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.9
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12434898; hg19: chr14-101762041;