ENST00000667966.1:n.269+4225T>A

Variant names:

• chr9-73543838-A-T
• rs278714
• ENST00000667966.1:n.269+4225T>A

Variant summary

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

The ENST00000667966.1(ENSG00000286840):​n.269+4225T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.845 in 152,078 control chromosomes in the GnomAD database, including 55,783 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 0.84 (55783 hom., cov: 33)
• Consequence: ENSG00000286840 ENST00000667966.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 3 publications found

Genes affected

ENSG00000286840 (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 (NFE) allele frequency at 95% confidence interval = 0.95 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000667966.1. 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
	ENSG00000286840	ENST00000667966.1		n.269+4225T>A		intron	N/A
	ENSG00000232590	ENST00000715871.1		n.182-34031A>T		intron	N/A
	ENSG00000232590	ENST00000715872.1		n.196-59526A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.845 AC: 128399 AN: 151960 Hom.: 55764 Cov.: 33

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.986

Gnomad AMR AF: 0.877

Gnomad ASJ AF: 0.909

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.921

Gnomad MID AF: 0.834

Gnomad NFE AF: 0.956

Gnomad OTH AF: 0.870

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

GnomAD4 genome AF: 0.845 AC: 128470 AN: 152078 Hom.: 55783 Cov.: 33 AF XY: 0.844 AC XY: 62751 AN XY: 74340

African (AFR) AF: 0.626 AC: 25937 AN: 41462

American (AMR) AF: 0.877 AC: 13400 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.909 AC: 3155 AN: 3470

East Asian (EAS) AF: 0.778 AC: 4032 AN: 5180

South Asian (SAS) AF: 0.872 AC: 4205 AN: 4822

European-Finnish (FIN) AF: 0.921 AC: 9758 AN: 10594

Middle Eastern (MID) AF: 0.849 AC: 248 AN: 292

European-Non Finnish (NFE) AF: 0.956 AC: 64995 AN: 67956

Other (OTH) AF: 0.872 AC: 1841 AN: 2112

Alfa AF: 0.896 Hom.: 3202

Bravo AF: 0.830

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.15
DANN	Benign	0.56
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs278714; hg19: chr9-76158754;