rs2193055

Variant names:

• chr17-72029572-T-G
• rs2193055
• ENST00000430908.8:n.284+749A>C

Variant summary

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

The ENST00000430908.8(ROCR):​n.284+749A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 151,988 control chromosomes in the GnomAD database, including 6,071 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 0.26 (6071 hom., cov: 31)
• Consequence: ROCR ENST00000430908.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.89

Genes affected

ROCR (HGNC:52946): (regulator of chondrogenesis RNA)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.479 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
ROCR	ENST00000430908.8	n.284+749A>C		intron_variant	Intron 1 of 3	2
ROCR	ENST00000540802.2	n.1130-3595A>C		intron_variant	Intron 3 of 5	4
ROCR	ENST00000543512.1	n.194+4327A>C		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39516 AN: 151868 Hom.: 6050 Cov.: 31

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.260 AC: 39576 AN: 151988 Hom.: 6071 Cov.: 31 AF XY: 0.259 AC XY: 19272 AN XY: 74292

Gnomad4 AFR AF: 0.404

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.495

Gnomad4 SAS AF: 0.344

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.239

Alfa AF: 0.209 Hom.: 864

Bravo AF: 0.264

Asia WGS AF: 0.486 AC: 1688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.064
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2193055; hg19: chr17-70025713;