ENST00000753888.1:n.95-76228A>G

Variant names:

• chr2-41046491-T-C
• rs17027130
• ENST00000753888.1:n.95-76228A>G

Variant summary

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

The ENST00000753888.1(ENSG00000298207):​n.95-76228A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.068 in 152,222 control chromosomes in the GnomAD database, including 663 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 0.068 (663 hom., cov: 32)
• Consequence: ENSG00000298207 ENST00000753888.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700
• Publications: 3 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.344 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298207	ENST00000753888.1		n.95-76228A>G		intron	N/A
	ENSG00000298207	ENST00000753889.1		n.95-76228A>G		intron	N/A
	ENSG00000298207	ENST00000753890.1		n.191-76228A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0680 AC: 10348 AN: 152104 Hom.: 659 Cov.: 32

Gnomad AFR AF: 0.0142

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.0735

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.0520

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0652

Gnomad OTH AF: 0.0684

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

GnomAD4 genome AF: 0.0680 AC: 10354 AN: 152222 Hom.: 663 Cov.: 32 AF XY: 0.0708 AC XY: 5269 AN XY: 74420

African (AFR) AF: 0.0142 AC: 591 AN: 41558

American (AMR) AF: 0.115 AC: 1756 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0735 AC: 255 AN: 3470

East Asian (EAS) AF: 0.358 AC: 1844 AN: 5154

South Asian (SAS) AF: 0.145 AC: 699 AN: 4830

European-Finnish (FIN) AF: 0.0520 AC: 551 AN: 10600

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0652 AC: 4434 AN: 67998

Other (OTH) AF: 0.0687 AC: 145 AN: 2112

Alfa AF: 0.0702 Hom.: 676

Bravo AF: 0.0697

Asia WGS AF: 0.214 AC: 743 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.1
DANN	Benign	0.43
PhyloP100		0.0070

Splicing

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

Other links and lift over

dbSNP: rs17027130; hg19: chr2-41273631;