chr9-19897266-T-C

Position:

• chr9-19897266-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.-390-6038A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 152,108 control chromosomes in the GnomAD database, including 8,188 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 0.31 (8188 hom., cov: 32)
• Consequence: SLC24A2 XM_017014592.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.281

Genes affected

SLC24A2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC24A2	XM_017014592.2	c.-390-6038A>G		intron_variant			XP_016870081.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47366 AN: 151988 Hom.: 8184 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.0912

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.312 AC: 47389 AN: 152108 Hom.: 8188 Cov.: 32 AF XY: 0.309 AC XY: 22962 AN XY: 74362

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.344

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.0918

Gnomad4 SAS AF: 0.245

Gnomad4 FIN AF: 0.393

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.293

Alfa AF: 0.374 Hom.: 14885

Bravo AF: 0.303

Asia WGS AF: 0.193 AC: 673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.43
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4977348; hg19: chr9-19897264;