rs12029080

Variant names:

• chr1-94587797-T-G
• rs12029080
• ENST00000413541.1:n.965-1035A>C

Variant summary

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

The ENST00000413541.1(SLC44A3-AS1):​n.965-1035A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 152,060 control chromosomes in the GnomAD database, including 5,065 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 0.24 (5065 hom., cov: 32)
• Consequence: SLC44A3-AS1 ENST00000413541.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.142
• Publications: 24 publications found

Genes affected

SLC44A3-AS1 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378861	XR_001738160.3	n.511+24184T>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC44A3-AS1	ENST00000413541.1	n.965-1035A>C		intron_variant	Intron 1 of 1	2
SLC44A3-AS1	ENST00000414374.2	n.439-1035A>C		intron_variant	Intron 2 of 2	3
ENSG00000301906	ENST00000782778.1	n.341+24184T>G		intron_variant	Intron 1 of 2
ENSG00000301906	ENST00000782779.1	n.331-7609T>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36742 AN: 151942 Hom.: 5069 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.242 AC: 36746 AN: 152060 Hom.: 5065 Cov.: 32 AF XY: 0.243 AC XY: 18068 AN XY: 74344

African (AFR) AF: 0.111 AC: 4610 AN: 41524

American (AMR) AF: 0.270 AC: 4124 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1493 AN: 3464

East Asian (EAS) AF: 0.258 AC: 1332 AN: 5164

South Asian (SAS) AF: 0.246 AC: 1187 AN: 4820

European-Finnish (FIN) AF: 0.292 AC: 3084 AN: 10572

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.295 AC: 20038 AN: 67928

Other (OTH) AF: 0.259 AC: 547 AN: 2108

Alfa AF: 0.282 Hom.: 24696

Bravo AF: 0.235

Asia WGS AF: 0.247 AC: 859 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.7
DANN	Benign	0.60
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs12029080; hg19: chr1-95053353;