rs2494750

Variant names:

• chr14-104796575-G-C
• rs2494750

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 0.85 in 152,186 control chromosomes in the GnomAD database, including 56,163 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 0.85 (56163 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.927 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: 0.850 AC: 129254 AN: 152068 Hom.: 56118 Cov.: 32

Gnomad AFR AF: 0.797

Gnomad AMI AF: 0.941

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.888

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.936

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.933

Gnomad OTH AF: 0.851

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

GnomAD4 genome AF: 0.850 AC: 129364 AN: 152186 Hom.: 56163 Cov.: 32 AF XY: 0.843 AC XY: 62745 AN XY: 74410

Gnomad4 AFR AF: 0.797

Gnomad4 AMR AF: 0.785

Gnomad4 ASJ AF: 0.888

Gnomad4 EAS AF: 0.336

Gnomad4 SAS AF: 0.664

Gnomad4 FIN AF: 0.936

Gnomad4 NFE AF: 0.933

Gnomad4 OTH AF: 0.848

Alfa AF: 0.897 Hom.: 7656

Bravo AF: 0.837

Asia WGS AF: 0.515 AC: 1795 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2494750; hg19: chr14-105262912;