chr1-94604485-T-C

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000414374.2. 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	ENST00000414374.2	TSL:3	n.439-17723A>G		intron	N/A
	ENSG00000301906	ENST00000782778.1		n.342-31306T>C		intron	N/A
	ENSG00000301906	ENST00000782779.1		n.430+8980T>C		intron	N/A

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 v4.9

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;