10-5244199-G-A

Variant names:

• chr10-5244199-G-A
• rs9423393
• ENST00000428920.3:n.285+9606G>A

Variant summary

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

The ENST00000428920.3(ENSG00000231039):​n.285+9606G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.602 in 151,978 control chromosomes in the GnomAD database, including 28,293 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 (28293 hom., cov: 32)
• Consequence: ENSG00000231039 ENST00000428920.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05
• Publications: 8 publications found

Genes affected

ENSG00000231039 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.86 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000428920.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000231039	ENST00000428920.3	TSL:3	n.285+9606G>A		intron	N/A
	ENSG00000231039	ENST00000757036.1		n.163+9606G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.602 AC: 91415 AN: 151860 Hom.: 28287 Cov.: 32

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.705

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.881

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.602 AC: 91461 AN: 151978 Hom.: 28293 Cov.: 32 AF XY: 0.609 AC XY: 45221 AN XY: 74310

African (AFR) AF: 0.459 AC: 19011 AN: 41418

American (AMR) AF: 0.661 AC: 10101 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.692 AC: 2400 AN: 3466

East Asian (EAS) AF: 0.881 AC: 4551 AN: 5166

South Asian (SAS) AF: 0.714 AC: 3438 AN: 4816

European-Finnish (FIN) AF: 0.660 AC: 6970 AN: 10554

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.629 AC: 42775 AN: 67962

Other (OTH) AF: 0.647 AC: 1366 AN: 2110

Alfa AF: 0.632 Hom.: 36632

Bravo AF: 0.599

Asia WGS AF: 0.768 AC: 2673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.3
DANN	Benign	0.72
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs9423393; hg19: chr10-5286162;