2-39890775-C-A

Variant names:

• chr2-39890775-C-A
• rs1159627
• ENST00000444629.6:n.138+21101C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000444629.6(SLC8A1-AS1):​n.138+21101C>A variant causes a intron 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 ENST00000444629.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.333
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000444629.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC8A1-AS1	ENST00000444629.6	TSL:3	n.138+21101C>A		intron	N/A
	SLC8A1-AS1	ENST00000599740.1	TSL:5	n.73+104250C>A		intron	N/A
	SLC8A1-AS1	ENST00000628471.2	TSL:5	n.396+38678C>A		intron	N/A

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

African (AFR) AF: 0.514 AC: 21217 AN: 41312

American (AMR) AF: 0.0713 AC: 1089 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0199 AC: 69 AN: 3470

East Asian (EAS) AF: 0.000964 AC: 5 AN: 5186

South Asian (SAS) AF: 0.0432 AC: 208 AN: 4820

European-Finnish (FIN) AF: 0.0136 AC: 144 AN: 10620

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0128 AC: 868 AN: 67992

Other (OTH) AF: 0.115 AC: 243 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.0
DANN	Benign	0.61
PhyloP100		0.33
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1159627; hg19: chr2-40117915;