rs2494750

Variant names:

• chr14-104796575-G-C
• rs2494750

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 0.85 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
• Publications: 26 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.797 AC: 33056 AN: 41478

American (AMR) AF: 0.785 AC: 12019 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.888 AC: 3081 AN: 3470

East Asian (EAS) AF: 0.336 AC: 1739 AN: 5168

South Asian (SAS) AF: 0.664 AC: 3204 AN: 4824

European-Finnish (FIN) AF: 0.936 AC: 9930 AN: 10608

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.933 AC: 63447 AN: 68014

Other (OTH) AF: 0.848 AC: 1793 AN: 2114

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
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs2494750; hg19: chr14-105262912;