rs7175404

Variant names:

• chr15-93493459-A-G
• rs7175404
• ENST00000543286.5:n.546-36778A>G

Variant summary

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

The ENST00000543286.5(ENSG00000257060):​n.546-36778A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 152,116 control chromosomes in the GnomAD database, including 6,857 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 0.27 (6857 hom., cov: 32)
• Consequence: ENSG00000257060 ENST00000543286.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.47
• Publications: 11 publications found

Genes affected

ENSG00000257060 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000543286.5. 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
	ENSG00000257060	ENST00000543286.5	TSL:2	n.546-36778A>G		intron	N/A
	ENSG00000257060	ENST00000553478.1	TSL:4	n.319-64013A>G		intron	N/A
	ENSG00000257060	ENST00000554105.6	TSL:4	n.499-36778A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40291 AN: 151998 Hom.: 6843 Cov.: 32

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.265 AC: 40350 AN: 152116 Hom.: 6857 Cov.: 32 AF XY: 0.270 AC XY: 20095 AN XY: 74378

African (AFR) AF: 0.449 AC: 18616 AN: 41476

American (AMR) AF: 0.280 AC: 4277 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 484 AN: 3468

East Asian (EAS) AF: 0.463 AC: 2396 AN: 5172

South Asian (SAS) AF: 0.409 AC: 1974 AN: 4828

European-Finnish (FIN) AF: 0.174 AC: 1840 AN: 10584

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.145 AC: 9888 AN: 68008

Other (OTH) AF: 0.268 AC: 565 AN: 2108

Alfa AF: 0.201 Hom.: 7893

Bravo AF: 0.280

Asia WGS AF: 0.452 AC: 1571 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.041
DANN	Benign	0.76
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs7175404; hg19: chr15-94036688;