ENST00000804476.1:n.111-35274C>T

Variant names:

• chr9-31669520-G-A
• rs2044401
• ENST00000804476.1:n.111-35274C>T

Variant summary

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

The ENST00000804476.1(ENSG00000304547):​n.111-35274C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 151,944 control chromosomes in the GnomAD database, including 3,938 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 0.23 (3938 hom., cov: 32)
• Consequence: ENSG00000304547 ENST00000804476.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02
• Publications: 2 publications found

Genes affected

ENSG00000304547 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.292 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
ENSG00000304547	ENST00000804476.1	n.111-35274C>T		intron_variant	Intron 1 of 2
ENSG00000304547	ENST00000804477.1	n.140-7961C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34442 AN: 151826 Hom.: 3926 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.227 AC: 34493 AN: 151944 Hom.: 3938 Cov.: 32 AF XY: 0.226 AC XY: 16767 AN XY: 74244

African (AFR) AF: 0.234 AC: 9702 AN: 41428

American (AMR) AF: 0.299 AC: 4564 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 779 AN: 3466

East Asian (EAS) AF: 0.137 AC: 705 AN: 5164

South Asian (SAS) AF: 0.130 AC: 628 AN: 4818

European-Finnish (FIN) AF: 0.213 AC: 2240 AN: 10534

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15177 AN: 67962

Other (OTH) AF: 0.252 AC: 531 AN: 2106

Alfa AF: 0.226 Hom.: 17771

Bravo AF: 0.237

Asia WGS AF: 0.135 AC: 468 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	11
DANN	Benign	0.62
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs2044401; hg19: chr9-31669518;