17-71963822-T-C

Variant names:

• chr17-71963822-T-C
• rs7214582
• ENST00000715472.1:n.237+222A>G

Variant summary

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

The ENST00000715472.1(ROCR):​n.237+222A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.947 in 152,268 control chromosomes in the GnomAD database, including 68,420 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 0.95 (68420 hom., cov: 32)
• Consequence: ROCR ENST00000715472.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.667
• Publications: 4 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.981 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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ROCR	ENST00000715472.1		n.237+222A>G		intron	N/A
	ROCR	ENST00000715473.1		n.133+222A>G		intron	N/A
	ROCR	ENST00000715474.1		n.253-11398A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.947 AC: 144134 AN: 152150 Hom.: 68364 Cov.: 32

Gnomad AFR AF: 0.989

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.953

Gnomad ASJ AF: 0.949

Gnomad EAS AF: 0.938

Gnomad SAS AF: 0.924

Gnomad FIN AF: 0.854

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.937

Gnomad OTH AF: 0.943

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

GnomAD4 genome AF: 0.947 AC: 144248 AN: 152268 Hom.: 68420 Cov.: 32 AF XY: 0.943 AC XY: 70217 AN XY: 74434

African (AFR) AF: 0.989 AC: 41108 AN: 41562

American (AMR) AF: 0.953 AC: 14567 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.949 AC: 3294 AN: 3472

East Asian (EAS) AF: 0.938 AC: 4855 AN: 5174

South Asian (SAS) AF: 0.923 AC: 4448 AN: 4818

European-Finnish (FIN) AF: 0.854 AC: 9058 AN: 10612

Middle Eastern (MID) AF: 0.939 AC: 276 AN: 294

European-Non Finnish (NFE) AF: 0.937 AC: 63742 AN: 68026

Other (OTH) AF: 0.943 AC: 1991 AN: 2112

Alfa AF: 0.942 Hom.: 107441

Bravo AF: 0.958

Asia WGS AF: 0.941 AC: 3273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	13
DANN	Benign	0.65
PhyloP100		0.67

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7214582;

hg19: chr17-69959963;