chr2-39890190-A-T

Position:

• chr2-39890190-A-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC8A1-AS1	ENST00000599740.1	n.73+103665A>T		intron_variant, non_coding_transcript_variant		5
SLC8A1-AS1	ENST00000628471.2	n.396+38093A>T		intron_variant, non_coding_transcript_variant		5
SLC8A1-AS1	ENST00000631142.2	n.401+20516A>T		intron_variant, non_coding_transcript_variant		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;