chr2-39890190-A-T

Variant names:

• chr2-39890190-A-T
• rs10490337
• ENST00000444629.6:n.138+20516A>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+20516A>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 ENST00000444629.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.509 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC8A1-AS1	ENST00000444629.6	TSL:3	n.138+20516A>T		intron	N/A
	SLC8A1-AS1	ENST00000599740.1	TSL:5	n.73+103665A>T		intron	N/A
	SLC8A1-AS1	ENST00000628471.2	TSL:5	n.396+38093A>T		intron	N/A

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

African (AFR) AF: 0.515 AC: 21322 AN: 41406

American (AMR) AF: 0.0711 AC: 1087 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0199 AC: 69 AN: 3472

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5180

South Asian (SAS) AF: 0.0433 AC: 209 AN: 4826

European-Finnish (FIN) AF: 0.0135 AC: 143 AN: 10606

Middle Eastern (MID) AF: 0.0685 AC: 20 AN: 292

European-Non Finnish (NFE) AF: 0.0127 AC: 867 AN: 68010

Other (OTH) AF: 0.114 AC: 242 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.4
DANN	Benign	0.54
PhyloP100		0.0020
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: rs10490337; hg19: chr2-40117330;