9-20220840-C-T

Position:

• chr9-20220840-C-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+80386G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.458 in 151,938 control chromosomes in the GnomAD database, including 17,627 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 0.46 (17627 hom., cov: 31)
• Consequence: SLC24A2 XM_017014592.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.525

Genes affected

SLC24A2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC24A2	XM_017014592.2	c.-529+80386G>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.459 AC: 69638 AN: 151820 Hom.: 17630 Cov.: 31

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.458 AC: 69638 AN: 151938 Hom.: 17627 Cov.: 31 AF XY: 0.451 AC XY: 33465 AN XY: 74266

Gnomad4 AFR AF: 0.300

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.580

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.543

Gnomad4 NFE AF: 0.587

Gnomad4 OTH AF: 0.461

Alfa AF: 0.537 Hom.: 11726

Bravo AF: 0.440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.64
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: rs321225; hg19: chr9-20220838;