4-4677180-A-G

Position:

• chr4-4677180-A-G

Variant summary

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

The XM_047416490.1(LOC124900165):​c.-9472+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: LOC124900165 XM_047416490.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.983 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124900165	XM_047416490.1	c.-9472+27638A>G		intron_variant			XP_047272446.1
STX18-AS1	NR_037888.1	n.818+27638A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STX18-AS1	ENST00000670162.1	n.1020+27638A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.991

Gnomad4 AMR AF: 0.965

Gnomad4 ASJ AF: 0.889

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.982

Gnomad4 FIN AF: 0.954

Gnomad4 NFE AF: 0.945

Gnomad4 OTH AF: 0.951

Alfa AF: 0.946 Hom.: 87453

Bravo AF: 0.963

Asia WGS AF: 0.992 AC: 3450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7675915; hg19: chr4-4678907;