2-41012940-G-T

Variant names:

• chr2-41012940-G-T
• rs12465519
• ENST00000753888.1:n.95-42677C>A

Variant summary

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

The ENST00000753888.1(ENSG00000298207):​n.95-42677C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 145,078 control chromosomes in the GnomAD database, including 11,775 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 0.35 (11775 hom., cov: 29)
• Consequence: ENSG00000298207 ENST00000753888.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0300
• Publications: 5 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.771 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.95-42677C>A		intron	N/A
	ENSG00000298207	ENST00000753889.1		n.95-42677C>A		intron	N/A
	ENSG00000298207	ENST00000753890.1		n.191-42677C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.346 AC: 50182 AN: 144970 Hom.: 11765 Cov.: 29

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.791

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.457

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.346 AC: 50210 AN: 145078 Hom.: 11775 Cov.: 29 AF XY: 0.353 AC XY: 24979 AN XY: 70814

African (AFR) AF: 0.210 AC: 7931 AN: 37680

American (AMR) AF: 0.372 AC: 5509 AN: 14816

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1172 AN: 3442

East Asian (EAS) AF: 0.791 AC: 4049 AN: 5118

South Asian (SAS) AF: 0.312 AC: 1458 AN: 4674

European-Finnish (FIN) AF: 0.397 AC: 3961 AN: 9988

Middle Eastern (MID) AF: 0.461 AC: 129 AN: 280

European-Non Finnish (NFE) AF: 0.376 AC: 24896 AN: 66168

Other (OTH) AF: 0.366 AC: 737 AN: 2016

Alfa AF: 0.353 Hom.: 9737

Asia WGS AF: 0.534 AC: 1830 AN: 3426

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.71
PhyloP100		-0.030

Splicing

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

Other links and lift over

dbSNP: rs12465519; hg19: chr2-41240080; COSMIC: COSV70042668;