17-71952875-A-G

Variant names:

• chr17-71952875-A-G
• rs7217932
• ENST00000715472.1:n.238-451T>C

Variant summary

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

The ENST00000715472.1(ROCR):​n.238-451T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 152,090 control chromosomes in the GnomAD database, including 17,882 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 0.47 (17882 hom., cov: 32)
• Consequence: ROCR ENST00000715472.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.45
• Publications: 28 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.797 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	ENST00000715472.1	n.238-451T>C		intron_variant	Intron 1 of 7
ROCR	ENST00000715473.1	n.134-451T>C		intron_variant	Intron 1 of 7
ROCR	ENST00000715474.1	n.253-451T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.469 AC: 71325 AN: 151972 Hom.: 17878 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.752

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.817

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.469 AC: 71348 AN: 152090 Hom.: 17882 Cov.: 32 AF XY: 0.475 AC XY: 35319 AN XY: 74354

African (AFR) AF: 0.290 AC: 12059 AN: 41514

American (AMR) AF: 0.574 AC: 8766 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1700 AN: 3472

East Asian (EAS) AF: 0.818 AC: 4232 AN: 5176

South Asian (SAS) AF: 0.522 AC: 2517 AN: 4824

European-Finnish (FIN) AF: 0.531 AC: 5616 AN: 10570

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.509 AC: 34577 AN: 67948

Other (OTH) AF: 0.495 AC: 1044 AN: 2108

Alfa AF: 0.503 Hom.: 75305

Bravo AF: 0.472

Asia WGS AF: 0.672 AC: 2335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.19
DANN	Benign	0.64
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs7217932; hg19: chr17-69949016;