7-138174020-A-G

Variant names:

• chr7-138174020-A-G
• rs10255295
• ENST00000834913.1:n.282+10518A>G

Variant summary

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

The ENST00000834913.1(ENSG00000225559):​n.282+10518A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 151,936 control chromosomes in the GnomAD database, including 910 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 0.10 (910 hom., cov: 31)
• Consequence: ENSG00000225559 ENST00000834913.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 4 publications found

Genes affected

ENSG00000225559 (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 = 0.117 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000834913.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000225559	ENST00000834913.1		n.282+10518A>G		intron	N/A
	ENSG00000225559	ENST00000834914.1		n.263-8811A>G		intron	N/A
	ENSG00000225559	ENST00000834915.1		n.261-8811A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15736 AN: 151818 Hom.: 908 Cov.: 31

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.0955

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.00309

Gnomad SAS AF: 0.0636

Gnomad FIN AF: 0.0825

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.104 AC: 15752 AN: 151936 Hom.: 910 Cov.: 31 AF XY: 0.0998 AC XY: 7412 AN XY: 74292

African (AFR) AF: 0.101 AC: 4178 AN: 41404

American (AMR) AF: 0.0953 AC: 1454 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 410 AN: 3470

East Asian (EAS) AF: 0.00310 AC: 16 AN: 5162

South Asian (SAS) AF: 0.0634 AC: 305 AN: 4808

European-Finnish (FIN) AF: 0.0825 AC: 873 AN: 10578

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8128 AN: 67950

Other (OTH) AF: 0.105 AC: 222 AN: 2108

Alfa AF: 0.115 Hom.: 1336

Bravo AF: 0.105

Asia WGS AF: 0.0440 AC: 156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.7
DANN	Benign	0.65
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs10255295; hg19: chr7-137858766;