rs10490337

Variant names:

• chr2-39890190-A-T
• rs10490337
• ENST00000599740.1:n.73+103665A>T

Variant summary

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

The ENST00000599740.1(SLC8A1-AS1):​n.73+103665A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,098 control chromosomes in the GnomAD database, including 5,705 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 0.16 (5705 hom., cov: 33)
• Consequence: SLC8A1-AS1 ENST00000599740.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200

Genes affected

SLC8A1-AS1 (HGNC:44102): (SLC8A1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC8A1-AS1	ENST00000599740.1	n.73+103665A>T		intron_variant	Intron 1 of 1	5
SLC8A1-AS1	ENST00000628471.2	n.396+38093A>T		intron_variant	Intron 3 of 5	5
SLC8A1-AS1	ENST00000631142.2	n.401+20516A>T		intron_variant	Intron 4 of 6	5

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23908 AN: 151982 Hom.: 5690 Cov.: 33

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0712

Gnomad ASJ AF: 0.0199

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0443

Gnomad FIN AF: 0.0135

Gnomad MID AF: 0.0669

Gnomad NFE AF: 0.0127

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.158 AC: 23964 AN: 152098 Hom.: 5705 Cov.: 33 AF XY: 0.154 AC XY: 11441 AN XY: 74366

Gnomad4 AFR AF: 0.515

Gnomad4 AMR AF: 0.0711

Gnomad4 ASJ AF: 0.0199

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0433

Gnomad4 FIN AF: 0.0135

Gnomad4 NFE AF: 0.0127

Gnomad4 OTH AF: 0.114

Alfa AF: 0.0978 Hom.: 415

Bravo AF: 0.179

Asia WGS AF: 0.0570 AC: 196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.4
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10490337; hg19: chr2-40117330;