4-4749545-T-G

Variant names:

• chr4-4749545-T-G
• rs7679624
• XM_047416485.1:c.-9471-11001T>G

Variant summary

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

The ENST00000670162.1(STX18-AS1):​n.1021-36724T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.74 in 151,896 control chromosomes in the GnomAD database, including 41,994 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 (41994 hom., cov: 30)
• Consequence: STX18-AS1 ENST00000670162.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.313
• Publications: 1 publications found

Genes affected

LOC124900165 (HGNC:):

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000670162.1. 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
	STX18-AS1	ENST00000670162.1		n.1021-36724T>G		intron	N/A
	STX18-AS1	ENST00000829246.1		n.764-70861T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.740 AC: 112316 AN: 151778 Hom.: 41955 Cov.: 30

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.814

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.619

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.740 AC: 112415 AN: 151896 Hom.: 41994 Cov.: 30 AF XY: 0.745 AC XY: 55288 AN XY: 74200

African (AFR) AF: 0.821 AC: 34023 AN: 41434

American (AMR) AF: 0.764 AC: 11672 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1992 AN: 3470

East Asian (EAS) AF: 0.845 AC: 4359 AN: 5160

South Asian (SAS) AF: 0.813 AC: 3866 AN: 4758

European-Finnish (FIN) AF: 0.745 AC: 7864 AN: 10550

Middle Eastern (MID) AF: 0.623 AC: 182 AN: 292

European-Non Finnish (NFE) AF: 0.682 AC: 46308 AN: 67946

Other (OTH) AF: 0.726 AC: 1528 AN: 2104

Alfa AF: 0.706 Hom.: 67448

Bravo AF: 0.742

Asia WGS AF: 0.835 AC: 2902 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.0
DANN	Benign	0.86
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs7679624; hg19: chr4-4751272;