rs2494750

Positions:

• chr14-104796575-G-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;