7-87067398-A-G

Variant names:

• chr7-87067398-A-G
• rs1476587
• ENST00000827229.1:n.364+6886A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000827229.1(ENSG00000307585):​n.364+6886A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,136 control chromosomes in the GnomAD database, including 1,375 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 0.13 (1375 hom., cov: 32)
• Consequence: ENSG00000307585 ENST00000827229.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.662
• Publications: 8 publications found

Genes affected

ENSG00000307585 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000827229.1. 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
	ENSG00000307585	ENST00000827229.1		n.364+6886A>G		intron	N/A
	ENSG00000307585	ENST00000827230.1		n.360+6886A>G		intron	N/A
	ENSG00000307585	ENST00000827231.1		n.359+6886A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19412 AN: 152018 Hom.: 1372 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.128 AC: 19448 AN: 152136 Hom.: 1375 Cov.: 32 AF XY: 0.130 AC XY: 9677 AN XY: 74386

African (AFR) AF: 0.119 AC: 4955 AN: 41522

American (AMR) AF: 0.142 AC: 2166 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 347 AN: 3468

East Asian (EAS) AF: 0.305 AC: 1580 AN: 5178

South Asian (SAS) AF: 0.155 AC: 745 AN: 4816

European-Finnish (FIN) AF: 0.158 AC: 1673 AN: 10590

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7620 AN: 67956

Other (OTH) AF: 0.112 AC: 237 AN: 2112

Alfa AF: 0.123 Hom.: 3375

Bravo AF: 0.128

Asia WGS AF: 0.253 AC: 874 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	8.8
DANN	Benign	0.92
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs1476587; hg19: chr7-86696714;