1-15788838-C-G

Variant names:

• chr1-15788838-C-G
• rs1472554
• ENST00000746505.1:n.347+3999G>C

Variant summary

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

The ENST00000746505.1(SPEN-AS1):​n.347+3999G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 151,794 control chromosomes in the GnomAD database, including 13,755 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 0.42 (13755 hom., cov: 31)
• Consequence: SPEN-AS1 ENST00000746505.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.454
• Publications: 6 publications found

Genes affected

SPEN-AS1 (HGNC:55937): (SPEN antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000746505.1. 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
	SPEN-AS1	ENST00000746505.1		n.347+3999G>C		intron	N/A
	SPEN-AS1	ENST00000746507.1		n.*74G>C		downstream_gene	N/A
	SPEN-AS1	ENST00000746508.1		n.*73G>C		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63082 AN: 151676 Hom.: 13733 Cov.: 31

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.0241

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.416 AC: 63151 AN: 151794 Hom.: 13755 Cov.: 31 AF XY: 0.414 AC XY: 30731 AN XY: 74194

African (AFR) AF: 0.499 AC: 20635 AN: 41370

American (AMR) AF: 0.407 AC: 6184 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1390 AN: 3470

East Asian (EAS) AF: 0.0240 AC: 124 AN: 5174

South Asian (SAS) AF: 0.422 AC: 2031 AN: 4810

European-Finnish (FIN) AF: 0.400 AC: 4205 AN: 10524

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.403 AC: 27390 AN: 67928

Other (OTH) AF: 0.402 AC: 848 AN: 2108

Alfa AF: 0.301 Hom.: 885

Bravo AF: 0.419

Asia WGS AF: 0.262 AC: 913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.4
DANN	Benign	0.33
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs1472554; hg19: chr1-16115333; COSMIC: COSV60029099;