rs7220150

Variant names:

• chr17-72212531-A-C
• rs7220150
• ENST00000532249.1:n.73+8115T>G

Your query was ambiguous. Multiple possible variants found:

• chr17-72212531-A-C
• chr17-72212531-A-G

Variant summary

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

The ENST00000532249.1(SOX9-AS1):​n.73+8115T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,078 control chromosomes in the GnomAD database, including 2,880 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 0.19 (2880 hom., cov: 32)
• Consequence: SOX9-AS1 ENST00000532249.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.254
• Publications: 0 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 = 0.364 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	ENST00000532249.1	n.73+8115T>G		intron_variant	Intron 1 of 2	3
ENSG00000288605	ENST00000674828.1	n.303+8115T>G		intron_variant	Intron 1 of 3
SOX9-AS1	ENST00000715469.1	n.114+8115T>G		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28328 AN: 151960 Hom.: 2874 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.186 AC: 28352 AN: 152078 Hom.: 2880 Cov.: 32 AF XY: 0.192 AC XY: 14312 AN XY: 74354

African (AFR) AF: 0.157 AC: 6512 AN: 41470

American (AMR) AF: 0.193 AC: 2945 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 515 AN: 3470

East Asian (EAS) AF: 0.378 AC: 1952 AN: 5164

South Asian (SAS) AF: 0.274 AC: 1318 AN: 4814

European-Finnish (FIN) AF: 0.197 AC: 2081 AN: 10588

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12368 AN: 67978

Other (OTH) AF: 0.197 AC: 416 AN: 2116

Alfa AF: 0.182 Hom.: 4359

Bravo AF: 0.185

Asia WGS AF: 0.311 AC: 1080 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	3.2
DANN	Benign	0.36
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs7220150; hg19: chr17-70208672;