ENST00000755956.1:n.429-17515G>A

Variant names:

• chr1-87482840-G-A
• rs17423694
• ENST00000755956.1:n.429-17515G>A

Variant summary

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

The ENST00000755956.1(ENSG00000298492):​n.429-17515G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0635 in 151,896 control chromosomes in the GnomAD database, including 353 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 0.063 (353 hom., cov: 33)
• Consequence: ENSG00000298492 ENST00000755956.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0290
• Publications: 2 publications found

Genes affected

ENSG00000298492 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0807 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755956.1. 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
	ENSG00000298492	ENST00000755956.1		n.429-17515G>A		intron	N/A
	ENSG00000298492	ENST00000755957.1		n.244+31739G>A		intron	N/A
	ENSG00000298492	ENST00000755958.1		n.404+31739G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0635 AC: 9639 AN: 151778 Hom.: 353 Cov.: 33

Gnomad AFR AF: 0.0392

Gnomad AMI AF: 0.0890

Gnomad AMR AF: 0.0602

Gnomad ASJ AF: 0.0815

Gnomad EAS AF: 0.00579

Gnomad SAS AF: 0.0403

Gnomad FIN AF: 0.0715

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0825

Gnomad OTH AF: 0.0679

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

GnomAD4 genome AF: 0.0635 AC: 9641 AN: 151896 Hom.: 353 Cov.: 33 AF XY: 0.0612 AC XY: 4540 AN XY: 74206

African (AFR) AF: 0.0391 AC: 1623 AN: 41476

American (AMR) AF: 0.0601 AC: 917 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0815 AC: 282 AN: 3462

East Asian (EAS) AF: 0.00581 AC: 30 AN: 5166

South Asian (SAS) AF: 0.0401 AC: 193 AN: 4814

European-Finnish (FIN) AF: 0.0715 AC: 752 AN: 10516

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0825 AC: 5601 AN: 67884

Other (OTH) AF: 0.0682 AC: 144 AN: 2112

Alfa AF: 0.0638 Hom.: 59

Bravo AF: 0.0619

Asia WGS AF: 0.0350 AC: 122 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.87
DANN	Benign	0.43
PhyloP100		-0.029

Splicing

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

Other links and lift over

dbSNP: rs17423694; hg19: chr1-87948523;