rs841338

Variant names:

• chr1-94677172-G-A
• rs841338
• ENST00000452922.5:n.808+2253C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-94677172-G-A
• chr1-94677172-G-C
• chr1-94677172-G-T

Variant summary

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

The ENST00000452922.5(SLC44A3-AS1):​n.808+2253C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.871 in 151,878 control chromosomes in the GnomAD database, including 59,605 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 0.87 (59605 hom., cov: 32)
• Consequence: SLC44A3-AS1 ENST00000452922.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.651
• 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.971 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000452922.5. 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
	SLC44A3-AS1	NR_104131.2		n.759+2253C>T		intron	N/A
	SLC44A3-AS1	NR_160779.1		n.512+2253C>T		intron	N/A
	SLC44A3-AS1	NR_160780.1		n.640+2253C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC44A3-AS1	ENST00000452922.5	TSL:1	n.808+2253C>T		intron	N/A
	SLC44A3-AS1	ENST00000414374.2	TSL:3	n.438+2253C>T		intron	N/A
	SLC44A3-AS1	ENST00000421997.5	TSL:3	n.566+2253C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.872 AC: 132278 AN: 151760 Hom.: 59592 Cov.: 32

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.993

Gnomad AMR AF: 0.910

Gnomad ASJ AF: 0.940

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.958

Gnomad FIN AF: 0.992

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.977

Gnomad OTH AF: 0.884

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

GnomAD4 genome AF: 0.871 AC: 132335 AN: 151878 Hom.: 59605 Cov.: 32 AF XY: 0.875 AC XY: 64939 AN XY: 74252

African (AFR) AF: 0.642 AC: 26415 AN: 41170

American (AMR) AF: 0.910 AC: 13923 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.940 AC: 3264 AN: 3472

East Asian (EAS) AF: 0.787 AC: 4067 AN: 5166

South Asian (SAS) AF: 0.959 AC: 4619 AN: 4818

European-Finnish (FIN) AF: 0.992 AC: 10539 AN: 10624

Middle Eastern (MID) AF: 0.956 AC: 281 AN: 294

European-Non Finnish (NFE) AF: 0.977 AC: 66460 AN: 68024

Other (OTH) AF: 0.884 AC: 1861 AN: 2106

Alfa AF: 0.956 Hom.: 41381

Bravo AF: 0.851

Asia WGS AF: 0.865 AC: 3012 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.4
DANN	Benign	0.64
PhyloP100		0.65

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: rs841338;

hg19: chr1-95142728;