rs2374459

Positions:

• chr2-43065694-G-A
• chr2-43065694-G-C
• chr2-43065694-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047446566.1(LOC107985876):​c.*2039C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 152,054 control chromosomes in the GnomAD database, including 23,364 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 0.54 (23364 hom., cov: 32)
• Consequence: LOC107985876 XM_047446566.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.03

Genes affected

LOC107985876 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985876	XM_047446566.1	c.*2039C>T		3_prime_UTR_variant	3/3
LOC107985876	XM_017005460.2	c.*1348C>T		3_prime_UTR_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81499 AN: 151936 Hom.: 23364 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.536 AC: 81524 AN: 152054 Hom.: 23364 Cov.: 32 AF XY: 0.539 AC XY: 40074 AN XY: 74346

Gnomad4 AFR AF: 0.336

Gnomad4 AMR AF: 0.597

Gnomad4 ASJ AF: 0.595

Gnomad4 EAS AF: 0.384

Gnomad4 SAS AF: 0.481

Gnomad4 FIN AF: 0.699

Gnomad4 NFE AF: 0.630

Gnomad4 OTH AF: 0.546

Alfa AF: 0.607 Hom.: 46453

Bravo AF: 0.521

Asia WGS AF: 0.435 AC: 1514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.028
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2374459; hg19: chr2-43292832;