rs1379023

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr2-40875823-G-C
• chr2-40875823-G-T

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000753888.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298207	ENST00000753888.1		n.150-38495C>G		intron	N/A
	ENSG00000298207	ENST00000753889.1		n.150-38495C>G		intron	N/A
	ENSG00000298207	ENST00000753890.1		n.246-38495C>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1379023;

hg19: chr2-41102963;