rs9423393

chr10-5244199-G-Achr10-5244199-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000428920.2(ENSG00000231039):n.236+9606G>A variant causes a intron, non coding transcript 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: ENST00000428920.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000428920.2	n.236+9606G>A		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.459

Gnomad4 AMR AF: 0.661

Gnomad4 ASJ AF: 0.692

Gnomad4 EAS AF: 0.881

Gnomad4 SAS AF: 0.714

Gnomad4 FIN AF: 0.660

Gnomad4 NFE AF: 0.629

Gnomad4 OTH AF: 0.647

Alfa AF: 0.638 Hom.: 28350

Bravo AF: 0.599

Asia WGS AF: 0.768 AC: 2673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	3.3
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9423393; hg19: chr10-5286162;