7-128265504-G-A

Variant names:

• chr7-128265504-G-A
• rs10954175
• ENST00000785446.1:n.187-152G>A

Variant summary

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

The ENST00000785446.1(ENSG00000302274):​n.187-152G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 152,068 control chromosomes in the GnomAD database, including 16,974 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 0.43 (16974 hom., cov: 32)
• Consequence: ENSG00000302274 ENST00000785446.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 3 publications found

Genes affected

ENSG00000302274 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.708 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000785446.1. 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
	ENSG00000302274	ENST00000785446.1		n.187-152G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65799 AN: 151950 Hom.: 16966 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.433 AC: 65809 AN: 152068 Hom.: 16974 Cov.: 32 AF XY: 0.437 AC XY: 32480 AN XY: 74312

African (AFR) AF: 0.138 AC: 5735 AN: 41516

American (AMR) AF: 0.511 AC: 7806 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1913 AN: 3466

East Asian (EAS) AF: 0.728 AC: 3761 AN: 5168

South Asian (SAS) AF: 0.547 AC: 2632 AN: 4816

European-Finnish (FIN) AF: 0.518 AC: 5471 AN: 10552

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.542 AC: 36796 AN: 67948

Other (OTH) AF: 0.473 AC: 998 AN: 2112

Alfa AF: 0.474 Hom.: 7630

Bravo AF: 0.415

Asia WGS AF: 0.626 AC: 2174 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.086
DANN	Benign	0.48
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10954175; hg19: chr7-127905557;