rs7694974

chr4-4685910-A-Gchr4-4685910-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047416490.1(LOC124900165):c.-9472+36368A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 152,006 control chromosomes in the GnomAD database, including 23,742 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 0.56 (23742 hom., cov: 33)
• Consequence: LOC124900165 XM_047416490.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163

Genes affected

LOC124900165 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124900165	XM_047416490.1	c.-9472+36368A>G		intron_variant
STX18-AS1	NR_037888.1	n.819-19763A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STX18-AS1	ENST00000670162.1	n.1020+36368A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84430 AN: 151888 Hom.: 23720 Cov.: 33

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.556 AC: 84491 AN: 152006 Hom.: 23742 Cov.: 33 AF XY: 0.556 AC XY: 41307 AN XY: 74290

Gnomad4 AFR AF: 0.621

Gnomad4 AMR AF: 0.518

Gnomad4 ASJ AF: 0.482

Gnomad4 EAS AF: 0.529

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.612

Gnomad4 NFE AF: 0.532

Gnomad4 OTH AF: 0.522

Alfa AF: 0.526 Hom.: 9699

Bravo AF: 0.552

Asia WGS AF: 0.531 AC: 1851 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	5.0
Dann	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7694974; hg19: chr4-4687637;