rs12451750

Variant names:

• chr17-71849137-G-A
• rs12451750
• ENST00000715471.1:n.332+9484C>T

Variant summary

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

The ENST00000715471.1(ROCR):​n.332+9484C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 152,138 control chromosomes in the GnomAD database, including 1,657 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 0.13 (1657 hom., cov: 32)
• Consequence: ROCR ENST00000715471.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.352
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.217 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	ENST00000715471.1	n.332+9484C>T		intron_variant	Intron 4 of 4
ROCR	ENST00000715472.1	n.748+9484C>T		intron_variant	Intron 7 of 7
ROCR	ENST00000715475.1	n.118-2289C>T		intron_variant	Intron 2 of 3
ROCR	ENST00000715476.1	n.491-18897C>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19177 AN: 152022 Hom.: 1658 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.0527

Gnomad EAS AF: 0.0733

Gnomad SAS AF: 0.0926

Gnomad FIN AF: 0.0889

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.0682

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.126 AC: 19180 AN: 152138 Hom.: 1657 Cov.: 32 AF XY: 0.128 AC XY: 9539 AN XY: 74388

African (AFR) AF: 0.221 AC: 9162 AN: 41466

American (AMR) AF: 0.204 AC: 3123 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0527 AC: 183 AN: 3472

East Asian (EAS) AF: 0.0731 AC: 379 AN: 5186

South Asian (SAS) AF: 0.0927 AC: 447 AN: 4824

European-Finnish (FIN) AF: 0.0889 AC: 943 AN: 10602

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 292

European-Non Finnish (NFE) AF: 0.0682 AC: 4638 AN: 67998

Other (OTH) AF: 0.122 AC: 258 AN: 2114

Alfa AF: 0.0865 Hom.: 374

Bravo AF: 0.140

Asia WGS AF: 0.0840 AC: 293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.56
DANN	Benign	0.40
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs12451750; hg19: chr17-69845278;