9-124119169-C-T

Variant names:

• chr9-124119169-C-T
• rs1463729
• ENST00000736080.1:n.285-4302G>A

Variant summary

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

The ENST00000736080.1(ENSG00000296076):​n.285-4302G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.619 in 152,198 control chromosomes in the GnomAD database, including 29,720 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 0.62 (29720 hom., cov: 34)
• Consequence: ENSG00000296076 ENST00000736080.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207
• Publications: 19 publications found

Genes affected

ENSG00000296076 (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 (AFR) allele frequency at 95% confidence interval = 0.732 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
ENSG00000296076	ENST00000736080.1	n.285-4302G>A		intron_variant	Intron 2 of 3
ENSG00000296076	ENST00000736081.1	n.174+6077G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.619 AC: 94144 AN: 152080 Hom.: 29686 Cov.: 34

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.614

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

GnomAD4 genome AF: 0.619 AC: 94226 AN: 152198 Hom.: 29720 Cov.: 34 AF XY: 0.616 AC XY: 45824 AN XY: 74410

African (AFR) AF: 0.739 AC: 30706 AN: 41528

American (AMR) AF: 0.578 AC: 8836 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1912 AN: 3468

East Asian (EAS) AF: 0.468 AC: 2424 AN: 5176

South Asian (SAS) AF: 0.449 AC: 2169 AN: 4828

European-Finnish (FIN) AF: 0.615 AC: 6523 AN: 10598

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.581 AC: 39508 AN: 67992

Other (OTH) AF: 0.606 AC: 1280 AN: 2112

Alfa AF: 0.584 Hom.: 107612

Bravo AF: 0.626

Asia WGS AF: 0.449 AC: 1562 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.40
DANN	Benign	0.44
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs1463729; hg19: chr9-126881448;