chr9-108237036-C-T

Variant names:

• chr9-108237036-C-T
• rs10120476
• ENST00000794224.1:n.346+9690G>A

Variant summary

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

The ENST00000794224.1(ENSG00000230030):​n.346+9690G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0339 in 152,202 control chromosomes in the GnomAD database, including 199 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 0.034 (199 hom., cov: 32)
• Consequence: ENSG00000230030 ENST00000794224.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.146
• Publications: 1 publications found

Genes affected

ENSG00000230030 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0882 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376214	XR_001746881.2	n.720+73630G>A		intron_variant	Intron 4 of 4
LOC105376214	XR_001746882.2	n.720+73630G>A		intron_variant	Intron 4 of 5
LOC105376214	XR_007061722.1	n.720+73630G>A		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000230030	ENST00000794224.1	n.346+9690G>A		intron_variant	Intron 3 of 3
ENSG00000230030	ENST00000794225.1	n.265-21537G>A		intron_variant	Intron 1 of 2
ENSG00000230030	ENST00000794226.1	n.342+9690G>A		intron_variant	Intron 2 of 2
ENSG00000230030	ENST00000794227.1	n.260-21537G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0338 AC: 5134 AN: 152084 Hom.: 197 Cov.: 32

Gnomad AFR AF: 0.0906

Gnomad AMI AF: 0.00659

Gnomad AMR AF: 0.0427

Gnomad ASJ AF: 0.00634

Gnomad EAS AF: 0.0193

Gnomad SAS AF: 0.0165

Gnomad FIN AF: 0.000378

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00670

Gnomad OTH AF: 0.0287

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

GnomAD4 genome AF: 0.0339 AC: 5157 AN: 152202 Hom.: 199 Cov.: 32 AF XY: 0.0325 AC XY: 2420 AN XY: 74398

African (AFR) AF: 0.0906 AC: 3761 AN: 41512

American (AMR) AF: 0.0434 AC: 663 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.00634 AC: 22 AN: 3470

East Asian (EAS) AF: 0.0193 AC: 100 AN: 5178

South Asian (SAS) AF: 0.0168 AC: 81 AN: 4832

European-Finnish (FIN) AF: 0.000378 AC: 4 AN: 10596

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.00671 AC: 456 AN: 68004

Other (OTH) AF: 0.0284 AC: 60 AN: 2112

Alfa AF: 0.0203 Hom.: 29

Bravo AF: 0.0419

Asia WGS AF: 0.0280 AC: 98 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.6
DANN	Benign	0.39
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs10120476; hg19: chr9-110999316;