ENST00000413541.1:n.965-158C>A

Variant names:

• chr1-94586920-G-T
• rs2022309
• ENST00000413541.1:n.965-158C>A

Variant summary

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

The ENST00000413541.1(SLC44A3-AS1):​n.965-158C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,030 control chromosomes in the GnomAD database, including 4,911 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 (4911 hom., cov: 33)
• Consequence: SLC44A3-AS1 ENST00000413541.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.14
• Publications: 14 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378861	XR_001738160.3	n.511+23307G>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC44A3-AS1	ENST00000413541.1	n.965-158C>A		intron_variant	Intron 1 of 1	2
SLC44A3-AS1	ENST00000414374.2	n.439-158C>A		intron_variant	Intron 2 of 2	3
ENSG00000301906	ENST00000782778.1	n.341+23307G>T		intron_variant	Intron 1 of 2
ENSG00000301906	ENST00000782779.1	n.331-8486G>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35839 AN: 151910 Hom.: 4916 Cov.: 33

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.236 AC: 35838 AN: 152030 Hom.: 4911 Cov.: 33 AF XY: 0.235 AC XY: 17491 AN XY: 74314

African (AFR) AF: 0.101 AC: 4183 AN: 41482

American (AMR) AF: 0.269 AC: 4106 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1497 AN: 3468

East Asian (EAS) AF: 0.257 AC: 1332 AN: 5174

South Asian (SAS) AF: 0.245 AC: 1182 AN: 4816

European-Finnish (FIN) AF: 0.252 AC: 2659 AN: 10560

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

European-Non Finnish (NFE) AF: 0.294 AC: 20008 AN: 67942

Other (OTH) AF: 0.256 AC: 540 AN: 2108

Alfa AF: 0.277 Hom.: 19678

Bravo AF: 0.231

Asia WGS AF: 0.246 AC: 855 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	13
DANN	Benign	0.42
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs2022309; hg19: chr1-95052476;