5-30661466-G-T

Variant names:

• chr5-30661466-G-T
• rs9292394
• ENST00000667165.1:n.138-17135C>A

Variant summary

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

The ENST00000667165.1(ENSG00000287940):​n.138-17135C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.674 in 151,948 control chromosomes in the GnomAD database, including 36,208 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 0.67 (36208 hom., cov: 31)
• Consequence: ENSG00000287940 ENST00000667165.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.121
• Publications: 6 publications found

Genes affected

ENSG00000287940 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.82 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000667165.1. 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
	ENSG00000287940	ENST00000667165.1		n.138-17135C>A		intron	N/A
	ENSG00000287940	ENST00000716667.1		n.229-17135C>A		intron	N/A
	ENSG00000287940	ENST00000716668.1		n.219-17135C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.674 AC: 102317 AN: 151826 Hom.: 36195 Cov.: 31

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.827

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.745

Gnomad EAS AF: 0.841

Gnomad SAS AF: 0.836

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.704

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

GnomAD4 genome AF: 0.674 AC: 102348 AN: 151948 Hom.: 36208 Cov.: 31 AF XY: 0.677 AC XY: 50284 AN XY: 74248

African (AFR) AF: 0.433 AC: 17953 AN: 41428

American (AMR) AF: 0.708 AC: 10807 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.745 AC: 2582 AN: 3466

East Asian (EAS) AF: 0.841 AC: 4317 AN: 5136

South Asian (SAS) AF: 0.836 AC: 4024 AN: 4814

European-Finnish (FIN) AF: 0.728 AC: 7682 AN: 10548

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.773 AC: 52516 AN: 67968

Other (OTH) AF: 0.709 AC: 1495 AN: 2110

Alfa AF: 0.743 Hom.: 194758

Bravo AF: 0.662

Asia WGS AF: 0.816 AC: 2837 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.46
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs9292394; hg19: chr5-30661573;