rs7046901

Positions:

• chr9-20246896-A-G
• chr9-20246896-A-T

Variant summary

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

The XM_017014592.2(SLC24A2):​c.-529+54330T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 152,166 control chromosomes in the GnomAD database, including 4,960 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 0.21 (4960 hom., cov: 32)
• Consequence: SLC24A2 XM_017014592.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.507

Genes affected

SLC24A2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC24A2	XM_017014592.2	c.-529+54330T>C		intron_variant			XP_016870081.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32490 AN: 152050 Hom.: 4945 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.0720

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0919

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.214 AC: 32538 AN: 152166 Hom.: 4960 Cov.: 32 AF XY: 0.224 AC XY: 16654 AN XY: 74396

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.0720

Gnomad4 EAS AF: 0.559

Gnomad4 SAS AF: 0.452

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.0919

Gnomad4 OTH AF: 0.219

Alfa AF: 0.127 Hom.: 2688

Bravo AF: 0.227

Asia WGS AF: 0.527 AC: 1835 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	0.48
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7046901; hg19: chr9-20246894; COSMIC: COSV60340749;