rs2154294

Positions:

• chr14-42186072-A-G
• chr14-42186072-A-T

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 0.554 in 151,726 control chromosomes in the GnomAD database, including 23,471 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 0.55 (23471 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.14

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.799 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: 0.554 AC: 84008 AN: 151608 Hom.: 23450 Cov.: 31

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.554 AC: 84072 AN: 151726 Hom.: 23471 Cov.: 31 AF XY: 0.562 AC XY: 41648 AN XY: 74134

Gnomad4 AFR AF: 0.557

Gnomad4 AMR AF: 0.549

Gnomad4 ASJ AF: 0.487

Gnomad4 EAS AF: 0.820

Gnomad4 SAS AF: 0.607

Gnomad4 FIN AF: 0.600

Gnomad4 NFE AF: 0.527

Gnomad4 OTH AF: 0.548

Alfa AF: 0.539 Hom.: 46210

Bravo AF: 0.544

Asia WGS AF: 0.680 AC: 2363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.3
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2154294; hg19: chr14-42655275;