14-101295704-C-G

Variant names:

• chr14-101295704-C-G
• rs12434898

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 0.227 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
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.299 AC: 12419 AN: 41544

American (AMR) AF: 0.198 AC: 3028 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 699 AN: 3470

East Asian (EAS) AF: 0.114 AC: 593 AN: 5184

South Asian (SAS) AF: 0.216 AC: 1042 AN: 4826

European-Finnish (FIN) AF: 0.304 AC: 3224 AN: 10602

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12946 AN: 67996

Other (OTH) AF: 0.196 AC: 414 AN: 2112

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
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs12434898; hg19: chr14-101762041;