rs2193055

Positions:

• chr17-72029572-T-G

Variant summary

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

The ENST00000540802.2(ROCR):​n.1130-3595A>C variant causes a intron, non coding transcript 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 ENST00000540802.2 intron, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ROCR	ENST00000540802.2	n.1130-3595A>C		intron_variant, non_coding_transcript_variant		4

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;