2-40875823-G-C

Variant names:

• chr2-40875823-G-C
• rs1379023
• ENST00000753888.1:n.150-38495C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000753888.1(ENSG00000298207):​n.150-38495C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.525 in 151,768 control chromosomes in the GnomAD database, including 21,426 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 0.53 (21426 hom., cov: 31)
• Consequence: ENSG00000298207 ENST00000753888.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82
• Publications: 1 publications found

Genes affected

ENSG00000298207 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374497	XR_001739421.3	n.60-38495C>G		intron_variant	Intron 1 of 3
LOC105374497	XR_001739422.1	n.1508+17723C>G		intron_variant	Intron 1 of 3
LOC105374497	XR_001739423.1	n.60-38495C>G		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298207	ENST00000753888.1	n.150-38495C>G		intron_variant	Intron 2 of 4
ENSG00000298207	ENST00000753889.1	n.150-38495C>G		intron_variant	Intron 2 of 5
ENSG00000298207	ENST00000753890.1	n.246-38495C>G		intron_variant	Intron 3 of 6
ENSG00000298207	ENST00000753891.1	n.246-38495C>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.525 AC: 79647 AN: 151648 Hom.: 21406 Cov.: 31

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.525 AC: 79713 AN: 151768 Hom.: 21426 Cov.: 31 AF XY: 0.524 AC XY: 38866 AN XY: 74192

African (AFR) AF: 0.608 AC: 25170 AN: 41430

American (AMR) AF: 0.569 AC: 8652 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.540 AC: 1871 AN: 3468

East Asian (EAS) AF: 0.617 AC: 3176 AN: 5146

South Asian (SAS) AF: 0.585 AC: 2816 AN: 4814

European-Finnish (FIN) AF: 0.428 AC: 4515 AN: 10546

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.473 AC: 32067 AN: 67846

Other (OTH) AF: 0.496 AC: 1045 AN: 2106

Alfa AF: 0.509 Hom.: 2486

Bravo AF: 0.540

Asia WGS AF: 0.581 AC: 2019 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.31
DANN	Benign	0.53
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1379023; hg19: chr2-41102963;