rs7175404

Positions:

• chr15-93493459-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000667030.1(ENSG00000257060):​n.237-2775A>G variant causes a intron, non coding transcript 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: ENST00000667030.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.47

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000667030.1	n.237-2775A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.449

Gnomad4 AMR AF: 0.280

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.463

Gnomad4 SAS AF: 0.409

Gnomad4 FIN AF: 0.174

Gnomad4 NFE AF: 0.145

Gnomad4 OTH AF: 0.268

Alfa AF: 0.180 Hom.: 4002

Bravo AF: 0.280

Asia WGS AF: 0.452 AC: 1571 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7175404; hg19: chr15-94036688;