17-72120683-G-GCGCA

Variant names:

• chr17-72120683-G-GCGCA
• rs3837814
• ENST00000533232.5:n.31+79_31+80insTGCG

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The ENST00000533232.5(SOX9-AS1):​n.31+79_31+80insTGCG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 150,846 control chromosomes in the GnomAD database, including 9,142 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.32 (9127 hom., cov: 0)
  • Exomes 𝑓: 0.18 (15 hom.)
• Consequence: SOX9-AS1 ENST00000533232.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.511
• Publications: 0 publications found

Genes affected

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

ENSG00000288605 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP6: Variant 17-72120683-G-GCGCA is Benign according to our data. Variant chr17-72120683-G-GCGCA is described in ClinVar as Benign. ClinVar VariationId is 1264490.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000533232.5. 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
	SOX9-AS1	NR_103737.1		n.31+79_31+80insTGCG		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOX9-AS1	ENST00000533232.5	TSL:1	n.31+79_31+80insTGCG		intron	N/A
	SOX9-AS1	ENST00000414600.1	TSL:3	n.96+21001_96+21002insTGCG		intron	N/A
	ENSG00000288605	ENST00000628742.2	TSL:5	n.147-35639_147-35638insTGCG		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.322 AC: 47873 AN: 148858 Hom.: 9127 Cov.: 0

Gnomad AFR AF: 0.0989

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.214

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.320

GnomAD4 exome AF: 0.180 AC: 342 AN: 1896 Hom.: 15 AF XY: 0.192 AC XY: 171 AN XY: 890

African (AFR) AF: 0.0714 AC: 6 AN: 84

American (AMR) AF: 0.250 AC: 12 AN: 48

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 20 AN: 160

East Asian (EAS) AF: 0.234 AC: 82 AN: 350

South Asian (SAS) AF: 0.222 AC: 4 AN: 18

European-Finnish (FIN) AF: 0.188 AC: 3 AN: 16

Middle Eastern (MID) AF: 0.100 AC: 1 AN: 10

European-Non Finnish (NFE) AF: 0.174 AC: 186 AN: 1068

Other (OTH) AF: 0.197 AC: 28 AN: 142

GnomAD4 genome AF: 0.321 AC: 47873 AN: 148950 Hom.: 9127 Cov.: 0 AF XY: 0.319 AC XY: 23138 AN XY: 72512

African (AFR) AF: 0.0986 AC: 4016 AN: 40712

American (AMR) AF: 0.406 AC: 6097 AN: 15002

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 889 AN: 3440

East Asian (EAS) AF: 0.498 AC: 2474 AN: 4972

South Asian (SAS) AF: 0.300 AC: 1399 AN: 4662

European-Finnish (FIN) AF: 0.332 AC: 3315 AN: 9988

Middle Eastern (MID) AF: 0.218 AC: 62 AN: 284

European-Non Finnish (NFE) AF: 0.428 AC: 28624 AN: 66924

Other (OTH) AF: 0.320 AC: 664 AN: 2074

Alfa AF: 0.149 Hom.: 349

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs3837814; hg19: chr17-70116824;