ENST00000826532.2:n.489-10302G>C

Variant names:

• chr9-24732484-G-C
• rs4977950
• ENST00000826532.2:n.489-10302G>C

Variant summary

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

The ENST00000826532.2(ENSG00000269957):​n.489-10302G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 151,858 control chromosomes in the GnomAD database, including 4,327 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 0.20 (4327 hom., cov: 32)
• Consequence: ENSG00000269957 ENST00000826532.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0690
• Publications: 7 publications found

Genes affected

ENSG00000269957 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.725 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
ENSG00000269957	ENST00000826532.2	n.489-10302G>C		intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30516 AN: 151740 Hom.: 4316 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.201 AC: 30536 AN: 151858 Hom.: 4327 Cov.: 32 AF XY: 0.213 AC XY: 15778 AN XY: 74206

African (AFR) AF: 0.154 AC: 6368 AN: 41436

American (AMR) AF: 0.337 AC: 5141 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 419 AN: 3472

East Asian (EAS) AF: 0.745 AC: 3833 AN: 5148

South Asian (SAS) AF: 0.352 AC: 1694 AN: 4818

European-Finnish (FIN) AF: 0.227 AC: 2381 AN: 10486

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10179 AN: 67936

Other (OTH) AF: 0.186 AC: 391 AN: 2098

Alfa AF: 0.157 Hom.: 282

Bravo AF: 0.209

Asia WGS AF: 0.468 AC: 1617 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.38
PhyloP100		-0.069

Splicing

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

Other links and lift over

dbSNP: rs4977950; hg19: chr9-24732482;