rs2193055

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000430908.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ROCR	ENST00000430908.8	TSL:2	n.284+749A>C		intron	N/A
	ROCR	ENST00000540802.2	TSL:4	n.1130-3595A>C		intron	N/A
	ROCR	ENST00000543512.1	TSL:3	n.194+4327A>C		intron	N/A

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

African (AFR) AF: 0.404 AC: 16727 AN: 41422

American (AMR) AF: 0.174 AC: 2653 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 586 AN: 3472

East Asian (EAS) AF: 0.495 AC: 2553 AN: 5156

South Asian (SAS) AF: 0.344 AC: 1654 AN: 4814

European-Finnish (FIN) AF: 0.167 AC: 1763 AN: 10568

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.189 AC: 12862 AN: 67966

Other (OTH) AF: 0.239 AC: 505 AN: 2110

Alfa AF: 0.214 Hom.: 928

Bravo AF: 0.264

Asia WGS AF: 0.486 AC: 1688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.064
DANN	Benign	0.41
PhyloP100		-3.9

Splicing

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

Other links and lift over

dbSNP: rs2193055; hg19: chr17-70025713;