17-72131395-T-C

Variant names:

• chr17-72131395-T-C
• rs9915657
• ENST00000414600.1:n.96+10290A>G

Variant summary

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

The ENST00000414600.1(SOX9-AS1):​n.96+10290A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 151,964 control chromosomes in the GnomAD database, including 18,682 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 0.49 (18682 hom., cov: 32)
• Consequence: SOX9-AS1 ENST00000414600.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0620
• Publications: 20 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SOX9-AS1	ENST00000414600.1	n.96+10290A>G		intron_variant	Intron 1 of 1	3
ENSG00000288605	ENST00000628742.2	n.146+41318A>G		intron_variant	Intron 2 of 6	5
ENSG00000288605	ENST00000674828.1	n.304-85871A>G		intron_variant	Intron 1 of 3
SOX9-AS1	ENST00000715469.1	n.510+41318A>G		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74076 AN: 151846 Hom.: 18651 Cov.: 32

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.488 AC: 74159 AN: 151964 Hom.: 18682 Cov.: 32 AF XY: 0.489 AC XY: 36304 AN XY: 74282

African (AFR) AF: 0.511 AC: 21154 AN: 41388

American (AMR) AF: 0.575 AC: 8780 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1137 AN: 3466

East Asian (EAS) AF: 0.786 AC: 4066 AN: 5174

South Asian (SAS) AF: 0.352 AC: 1693 AN: 4816

European-Finnish (FIN) AF: 0.418 AC: 4414 AN: 10562

Middle Eastern (MID) AF: 0.339 AC: 99 AN: 292

European-Non Finnish (NFE) AF: 0.463 AC: 31438 AN: 67972

Other (OTH) AF: 0.462 AC: 976 AN: 2112

Alfa AF: 0.475 Hom.: 35652

Bravo AF: 0.504

Asia WGS AF: 0.567 AC: 1973 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	12
DANN	Benign	0.71
PhyloP100		-0.062

Splicing

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

Other links and lift over

dbSNP: rs9915657; hg19: chr17-70127536;