chr4-4677180-A-G

Variant names:

• chr4-4677180-A-G
• rs7675915
• ENST00000610009.5:n.745+27638A>G

Variant summary

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

The ENST00000610009.5(STX18-AS1):​n.745+27638A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.962 in 152,218 control chromosomes in the GnomAD database, including 70,440 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 0.96 (70440 hom., cov: 30)
• Consequence: STX18-AS1 ENST00000610009.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280
• Publications: 4 publications found

Genes affected

STX18-AS1 (HGNC:48877): (STX18 antisense RNA 1 (head to head))

LOC124900165 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.983 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000610009.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STX18-AS1	NR_037888.1		n.818+27638A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STX18-AS1	ENST00000610009.5	TSL:1	n.745+27638A>G		intron	N/A
	STX18-AS1	ENST00000499430.7	TSL:2	n.1170+27638A>G		intron	N/A
	STX18-AS1	ENST00000608184.2	TSL:3	n.741+27638A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.962 AC: 146254 AN: 152100 Hom.: 70380 Cov.: 30

Gnomad AFR AF: 0.991

Gnomad AMI AF: 0.870

Gnomad AMR AF: 0.965

Gnomad ASJ AF: 0.889

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.982

Gnomad FIN AF: 0.954

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.945

Gnomad OTH AF: 0.950

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

GnomAD4 genome AF: 0.962 AC: 146373 AN: 152218 Hom.: 70440 Cov.: 30 AF XY: 0.963 AC XY: 71687 AN XY: 74426

African (AFR) AF: 0.991 AC: 41159 AN: 41544

American (AMR) AF: 0.965 AC: 14776 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.889 AC: 3086 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5134 AN: 5134

South Asian (SAS) AF: 0.982 AC: 4725 AN: 4812

European-Finnish (FIN) AF: 0.954 AC: 10123 AN: 10614

Middle Eastern (MID) AF: 0.966 AC: 284 AN: 294

European-Non Finnish (NFE) AF: 0.945 AC: 64288 AN: 68024

Other (OTH) AF: 0.951 AC: 2008 AN: 2112

Alfa AF: 0.948 Hom.: 123469

Bravo AF: 0.963

Asia WGS AF: 0.992 AC: 3450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.2
DANN	Benign	0.73
PhyloP100		0.028

Splicing

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

Other links and lift over

dbSNP: rs7675915; hg19: chr4-4678907;