9-21035308-G-T

Variant names:

• chr9-21035308-G-T
• rs7867456
• ENST00000726232.1:n.372+1812G>T

Variant summary

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

The ENST00000726232.1(ENSG00000294829):​n.372+1812G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.599 in 151,992 control chromosomes in the GnomAD database, including 27,534 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 0.60 (27534 hom., cov: 32)
• Consequence: ENSG00000294829 ENST00000726232.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.687
• Publications: 8 publications found

Genes affected

ENSG00000294829 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.665 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
ENSG00000294829	ENST00000726232.1	n.372+1812G>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.599 AC: 90958 AN: 151874 Hom.: 27522 Cov.: 32

Gnomad AFR AF: 0.550

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.599 AC: 90995 AN: 151992 Hom.: 27534 Cov.: 32 AF XY: 0.598 AC XY: 44436 AN XY: 74282

African (AFR) AF: 0.549 AC: 22739 AN: 41424

American (AMR) AF: 0.490 AC: 7482 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.636 AC: 2208 AN: 3472

East Asian (EAS) AF: 0.684 AC: 3546 AN: 5182

South Asian (SAS) AF: 0.565 AC: 2721 AN: 4818

European-Finnish (FIN) AF: 0.637 AC: 6722 AN: 10554

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.642 AC: 43655 AN: 67958

Other (OTH) AF: 0.569 AC: 1201 AN: 2110

Alfa AF: 0.621 Hom.: 3679

Bravo AF: 0.586

Asia WGS AF: 0.624 AC: 2172 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	11
DANN	Benign	0.72
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs7867456; hg19: chr9-21035307; COSMIC: COSV72217567;