18-9031721-A-G

Variant names:

• chr18-9031721-A-G
• rs7407664
• ENST00000827765.1:n.265-11358T>C

Variant summary

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

The ENST00000827765.1(ENSG00000288939):​n.265-11358T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0316 in 152,172 control chromosomes in the GnomAD database, including 193 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 0.032 (193 hom., cov: 30)
• Consequence: ENSG00000288939 ENST00000827765.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140
• Publications: 2 publications found

Genes affected

ENSG00000288939 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000827765.1. 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
	ENSG00000288939	ENST00000827765.1		n.265-11358T>C		intron	N/A
	ENSG00000288939	ENST00000827766.1		n.143-11358T>C		intron	N/A
	ENSG00000307687	ENST00000827902.1		n.89+28061A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0315 AC: 4794 AN: 152052 Hom.: 192 Cov.: 30

Gnomad AFR AF: 0.00790

Gnomad AMI AF: 0.00769

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.00750

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.0274

Gnomad FIN AF: 0.0153

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0342

Gnomad OTH AF: 0.0292

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

GnomAD4 genome AF: 0.0316 AC: 4804 AN: 152172 Hom.: 193 Cov.: 30 AF XY: 0.0318 AC XY: 2369 AN XY: 74392

African (AFR) AF: 0.00787 AC: 327 AN: 41532

American (AMR) AF: 0.114 AC: 1739 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.00750 AC: 26 AN: 3468

East Asian (EAS) AF: 0.00212 AC: 11 AN: 5184

South Asian (SAS) AF: 0.0272 AC: 131 AN: 4822

European-Finnish (FIN) AF: 0.0153 AC: 162 AN: 10604

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0342 AC: 2328 AN: 67980

Other (OTH) AF: 0.0289 AC: 61 AN: 2112

Alfa AF: 0.0145 Hom.: 10

Bravo AF: 0.0395

Asia WGS AF: 0.0230 AC: 78 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.8
DANN	Benign	0.28
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs7407664; hg19: chr18-9031719;