rs1558748

Variant names:

• chr17-72070361-T-C
• rs1558748
• ENST00000662263.1:n.1214A>G

Variant summary

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

The ENST00000662263.1(SOX9-AS1):​n.1214A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 152,096 control chromosomes in the GnomAD database, including 8,562 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 0.30 (8562 hom., cov: 31)
• Consequence: SOX9-AS1 ENST00000662263.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0520
• Publications: 4 publications found

Genes affected

SOX9-AS1 (HGNC:49321): (SOX9 antisense RNA 1)

ENSG00000288605 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000662263.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOX9-AS1	ENST00000662263.1		n.1214A>G		non_coding_transcript_exon	Exon 5 of 5
	ENSG00000288605	ENST00000602213.5	TSL:5	n.685+11560A>G		intron	N/A
	ENSG00000288605	ENST00000628742.2	TSL:5	n.615+702A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45953 AN: 151978 Hom.: 8560 Cov.: 31

Gnomad AFR AF: 0.0820

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.302 AC: 45954 AN: 152096 Hom.: 8562 Cov.: 31 AF XY: 0.299 AC XY: 22241 AN XY: 74328

African (AFR) AF: 0.0817 AC: 3395 AN: 41534

American (AMR) AF: 0.324 AC: 4949 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 878 AN: 3472

East Asian (EAS) AF: 0.451 AC: 2323 AN: 5154

South Asian (SAS) AF: 0.330 AC: 1591 AN: 4816

European-Finnish (FIN) AF: 0.334 AC: 3531 AN: 10564

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.415 AC: 28188 AN: 67968

Other (OTH) AF: 0.301 AC: 634 AN: 2108

Alfa AF: 0.366 Hom.: 33917

Bravo AF: 0.290

Asia WGS AF: 0.399 AC: 1387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.1
DANN	Benign	0.37
PhyloP100		0.052

Splicing

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

Other links and lift over

dbSNP: rs1558748; hg19: chr17-70066502;