2-39888556-C-T

Variant names:

• chr2-39888556-C-T
• rs6721181
• ENST00000444629.6:n.138+18882C>T

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+18882C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0207 in 151,552 control chromosomes in the GnomAD database, including 89 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 0.021 (89 hom., cov: 31)
• Consequence: SLC8A1-AS1 ENST00000444629.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.818
• Publications: 3 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0699 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	ENST00000444629.6	n.138+18882C>T		intron_variant	Intron 2 of 5	3
SLC8A1-AS1	ENST00000599740.1	n.73+102031C>T		intron_variant	Intron 1 of 1	5
SLC8A1-AS1	ENST00000628471.2	n.396+36459C>T		intron_variant	Intron 3 of 5	5
SLC8A1-AS1	ENST00000631142.2	n.401+18882C>T		intron_variant	Intron 4 of 6	5

Frequencies

GnomAD3 genomes AF: 0.0207 AC: 3132 AN: 151434 Hom.: 89 Cov.: 31

Gnomad AFR AF: 0.0720

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00685

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000626

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00955

Gnomad NFE AF: 0.000383

Gnomad OTH AF: 0.0144

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

GnomAD4 genome AF: 0.0207 AC: 3139 AN: 151552 Hom.: 89 Cov.: 31 AF XY: 0.0200 AC XY: 1483 AN XY: 74074

African (AFR) AF: 0.0721 AC: 2976 AN: 41304

American (AMR) AF: 0.00671 AC: 102 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3460

East Asian (EAS) AF: 0.00 AC: 0 AN: 5130

South Asian (SAS) AF: 0.000417 AC: 2 AN: 4792

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10538

Middle Eastern (MID) AF: 0.0103 AC: 3 AN: 292

European-Non Finnish (NFE) AF: 0.000383 AC: 26 AN: 67822

Other (OTH) AF: 0.0142 AC: 30 AN: 2108

Alfa AF: 0.0191 Hom.: 13

Bravo AF: 0.0238

Asia WGS AF: 0.00404 AC: 15 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	11
DANN	Benign	0.76
PhyloP100		0.82

Splicing

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

Other links and lift over

dbSNP: rs6721181; hg19: chr2-40115696;