ENST00000414374.2:n.439-17723A>G

Variant names:

• chr1-94604485-T-C
• rs7542900
• ENST00000414374.2:n.439-17723A>G

Variant summary

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

The ENST00000414374.2(SLC44A3-AS1):​n.439-17723A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.738 in 152,172 control chromosomes in the GnomAD database, including 42,389 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 0.74 (42389 hom., cov: 33)
• Consequence: SLC44A3-AS1 ENST00000414374.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300
• Publications: 25 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378861	XR_001738160.3	n.512-31306T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC44A3-AS1	ENST00000414374.2	n.439-17723A>G		intron_variant	Intron 2 of 2	3
ENSG00000301906	ENST00000782778.1	n.342-31306T>C		intron_variant	Intron 1 of 2
ENSG00000301906	ENST00000782779.1	n.430+8980T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.738 AC: 112251 AN: 152054 Hom.: 42378 Cov.: 33

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.887

Gnomad AMR AF: 0.719

Gnomad ASJ AF: 0.849

Gnomad EAS AF: 0.679

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.867

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.734

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

GnomAD4 genome AF: 0.738 AC: 112308 AN: 152172 Hom.: 42389 Cov.: 33 AF XY: 0.740 AC XY: 55058 AN XY: 74432

African (AFR) AF: 0.578 AC: 23979 AN: 41462

American (AMR) AF: 0.718 AC: 10984 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.849 AC: 2946 AN: 3470

East Asian (EAS) AF: 0.679 AC: 3510 AN: 5168

South Asian (SAS) AF: 0.776 AC: 3740 AN: 4822

European-Finnish (FIN) AF: 0.867 AC: 9200 AN: 10612

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.814 AC: 55351 AN: 68024

Other (OTH) AF: 0.734 AC: 1553 AN: 2116

Alfa AF: 0.781 Hom.: 161024

Bravo AF: 0.720

Asia WGS AF: 0.724 AC: 2518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.5
DANN	Benign	0.44
PhyloP100		-0.0030

Splicing

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

Other links and lift over

dbSNP: rs7542900; hg19: chr1-95070041; COSMIC: COSV59973914;