rs12951391

Variant names:

• chr17-71915441-C-T
• rs12951391
• ENST00000715472.1:n.311+36910G>A

Variant summary

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

The ENST00000715472.1(ROCR):​n.311+36910G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 151,730 control chromosomes in the GnomAD database, including 3,383 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 0.21 (3383 hom., cov: 32)
• Consequence: ROCR ENST00000715472.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.238
• Publications: 6 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715472.1. 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	ENST00000715472.1		n.311+36910G>A		intron	N/A
	ROCR	ENST00000715473.1		n.207+36910G>A		intron	N/A
	ROCR	ENST00000715474.1		n.326+36910G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31194 AN: 151612 Hom.: 3378 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.0936

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.0166

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.206 AC: 31208 AN: 151730 Hom.: 3383 Cov.: 32 AF XY: 0.204 AC XY: 15121 AN XY: 74112

African (AFR) AF: 0.234 AC: 9674 AN: 41362

American (AMR) AF: 0.150 AC: 2283 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1023 AN: 3466

East Asian (EAS) AF: 0.0162 AC: 84 AN: 5174

South Asian (SAS) AF: 0.191 AC: 917 AN: 4802

European-Finnish (FIN) AF: 0.206 AC: 2157 AN: 10474

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.214 AC: 14515 AN: 67940

Other (OTH) AF: 0.194 AC: 408 AN: 2104

Alfa AF: 0.210 Hom.: 14916

Bravo AF: 0.199

Asia WGS AF: 0.105 AC: 365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.53
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs12951391; hg19: chr17-69911582;