rs2093746

Positions:

• chr14-89760907-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 0.64 in 151,738 control chromosomes in the GnomAD database, including 31,359 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 0.64 (31359 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.720

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.709 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: 0.640 AC: 97031 AN: 151620 Hom.: 31342 Cov.: 30

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.619

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.655

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

GnomAD4 genome AF: 0.640 AC: 97099 AN: 151738 Hom.: 31359 Cov.: 30 AF XY: 0.640 AC XY: 47415 AN XY: 74114

Gnomad4 AFR AF: 0.568

Gnomad4 AMR AF: 0.720

Gnomad4 ASJ AF: 0.768

Gnomad4 EAS AF: 0.487

Gnomad4 SAS AF: 0.637

Gnomad4 FIN AF: 0.658

Gnomad4 NFE AF: 0.668

Gnomad4 OTH AF: 0.654

Alfa AF: 0.653 Hom.: 4045

Bravo AF: 0.641

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.85
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2093746; hg19: chr14-90227251;