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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000413541.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC44A3-AS1	ENST00000413541.1	TSL:2	n.965-1035A>C		intron	N/A
	SLC44A3-AS1	ENST00000414374.2	TSL:3	n.439-1035A>C		intron	N/A
	ENSG00000301906	ENST00000782778.1		n.341+24184T>G		intron	N/A

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 v4.9

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;