rs2022309

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.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC44A3-AS1	ENST00000413541.1	TSL:2	n.965-158C>A		intron	N/A
	SLC44A3-AS1	ENST00000414374.2	TSL:3	n.439-158C>A		intron	N/A
	ENSG00000301906	ENST00000782778.1		n.341+23307G>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2022309;

hg19: chr1-95052476;