9-20287950-T-C

Position:

• chr9-20287950-T-C

Variant summary

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

The XM_017014592.2(SLC24A2):​c.-529+13276A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.616 in 152,050 control chromosomes in the GnomAD database, including 30,698 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 (30698 hom., cov: 32)
• Consequence: SLC24A2 XM_017014592.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.61

Genes affected

SLC24A2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC24A2	XM_017014592.2	c.-529+13276A>G		intron_variant			XP_016870081.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93513 AN: 151932 Hom.: 30639 Cov.: 32

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.927

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.624

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

GnomAD4 genome AF: 0.616 AC: 93631 AN: 152050 Hom.: 30698 Cov.: 32 AF XY: 0.622 AC XY: 46197 AN XY: 74294

Gnomad4 AFR AF: 0.790

Gnomad4 AMR AF: 0.679

Gnomad4 ASJ AF: 0.604

Gnomad4 EAS AF: 0.927

Gnomad4 SAS AF: 0.828

Gnomad4 FIN AF: 0.461

Gnomad4 NFE AF: 0.482

Gnomad4 OTH AF: 0.628

Alfa AF: 0.531 Hom.: 30391

Bravo AF: 0.634

Asia WGS AF: 0.861 AC: 2996 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	11
DANN	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7026582; hg19: chr9-20287948; COSMIC: COSV60341039;