rs1159627

chr2-39890775-C-Achr2-39890775-C-Gchr2-39890775-C-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+104250C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 151,988 control chromosomes in the GnomAD database, including 5,644 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 (5644 hom., cov: 33)
• Consequence: SLC8A1-AS1 ENST00000599740.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.333

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=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC8A1-AS1	ENST00000599740.1	n.73+104250C>A		intron_variant, non_coding_transcript_variant		5
SLC8A1-AS1	ENST00000628471.2	n.396+38678C>A		intron_variant, non_coding_transcript_variant		5
SLC8A1-AS1	ENST00000631142.2	n.401+21101C>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23808 AN: 151870 Hom.: 5628 Cov.: 33

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0713

Gnomad ASJ AF: 0.0199

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.0442

Gnomad FIN AF: 0.0136

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0128

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.157 AC: 23866 AN: 151988 Hom.: 5644 Cov.: 33 AF XY: 0.154 AC XY: 11408 AN XY: 74316

Gnomad4 AFR AF: 0.514

Gnomad4 AMR AF: 0.0713

Gnomad4 ASJ AF: 0.0199

Gnomad4 EAS AF: 0.000964

Gnomad4 SAS AF: 0.0432

Gnomad4 FIN AF: 0.0136

Gnomad4 NFE AF: 0.0128

Gnomad4 OTH AF: 0.115

Alfa AF: 0.00910 Hom.: 26

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	-0.79
Cadd	Benign	5.0
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1159627; hg19: chr2-40117915;