ENST00000404796.3:n.461-70908T>C

Variant names:

• chr9-21958525-T-C
• rs717326
• ENST00000404796.3:n.461-70908T>C

Variant summary

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

The ENST00000404796.3(ENSG00000264545):​n.461-70908T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,128 control chromosomes in the GnomAD database, including 1,416 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 0.12 (1416 hom., cov: 32)
• Consequence: ENSG00000264545 ENST00000404796.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.746
• Publications: 16 publications found

Genes affected

ENSG00000264545 (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 = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000264545	ENST00000404796.3	n.461-70908T>C		intron_variant	Intron 4 of 4	5

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18817 AN: 152010 Hom.: 1414 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.0908

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0957

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.124 AC: 18831 AN: 152128 Hom.: 1416 Cov.: 32 AF XY: 0.127 AC XY: 9466 AN XY: 74358

African (AFR) AF: 0.127 AC: 5277 AN: 41512

American (AMR) AF: 0.250 AC: 3819 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0908 AC: 315 AN: 3470

East Asian (EAS) AF: 0.129 AC: 668 AN: 5166

South Asian (SAS) AF: 0.161 AC: 775 AN: 4816

European-Finnish (FIN) AF: 0.110 AC: 1166 AN: 10584

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0957 AC: 6506 AN: 68000

Other (OTH) AF: 0.112 AC: 237 AN: 2110

Alfa AF: 0.123 Hom.: 873

Bravo AF: 0.137

Asia WGS AF: 0.149 AC: 517 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.64
PhyloP100		-0.75

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs717326; hg19: chr9-21958524;