rs10493874

Variant names:

• chr1-94800877-C-T
• rs10493874
• ENST00000452922.5:n.326+19079G>A

Variant summary

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

The ENST00000452922.5(SLC44A3-AS1):​n.326+19079G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 151,956 control chromosomes in the GnomAD database, including 24,737 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 0.56 (24737 hom., cov: 32)
• Consequence: SLC44A3-AS1 ENST00000452922.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.03
• Publications: 4 publications found

Genes affected

SLC44A3-AS1 (HGNC:):

SLC44A3-AS1 (HGNC:49057): (SLC44A3 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC44A3-AS1	NR_104131.2	n.277+19079G>A		intron_variant	Intron 1 of 4
SLC44A3-AS1	NR_160779.1	n.277+19079G>A		intron_variant	Intron 1 of 5
SLC44A3-AS1	NR_160780.1	n.277+19079G>A		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC44A3-AS1	ENST00000452922.5	n.326+19079G>A		intron_variant	Intron 1 of 4	1
SLC44A3-AS1	ENST00000414374.2	n.255+19079G>A		intron_variant	Intron 1 of 2	3
SLC44A3-AS1	ENST00000418366.2	n.264+19079G>A		intron_variant	Intron 1 of 5	5

Frequencies

GnomAD3 genomes AF: 0.560 AC: 85023 AN: 151838 Hom.: 24715 Cov.: 32

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.761

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.560 AC: 85091 AN: 151956 Hom.: 24737 Cov.: 32 AF XY: 0.561 AC XY: 41668 AN XY: 74254

African (AFR) AF: 0.398 AC: 16473 AN: 41440

American (AMR) AF: 0.585 AC: 8929 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.724 AC: 2508 AN: 3462

East Asian (EAS) AF: 0.421 AC: 2168 AN: 5154

South Asian (SAS) AF: 0.696 AC: 3350 AN: 4816

European-Finnish (FIN) AF: 0.614 AC: 6473 AN: 10548

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.634 AC: 43085 AN: 67962

Other (OTH) AF: 0.579 AC: 1222 AN: 2112

Alfa AF: 0.581 Hom.: 4443

Bravo AF: 0.550

Asia WGS AF: 0.554 AC: 1927 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.5
DANN	Benign	0.69
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs10493874; hg19: chr1-95266433;