rs3803833

Variant names:

• chr17-72022770-T-G
• rs3803833
• ENST00000430908.8:n.517-791A>C

Variant summary

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

The ENST00000430908.8(ROCR):​n.517-791A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,110 control chromosomes in the GnomAD database, including 1,342 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 0.12 (1342 hom., cov: 32)
• Consequence: ROCR ENST00000430908.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.455
• 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=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ROCR	NR_110876.1	n.235-791A>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ROCR	ENST00000430908.8	n.517-791A>C		intron_variant	Intron 3 of 3	2
ROCR	ENST00000540802.2	n.1362-791A>C		intron_variant	Intron 5 of 5	4
ROCR	ENST00000543512.1	n.195-791A>C		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17891 AN: 151992 Hom.: 1346 Cov.: 32

Gnomad AFR AF: 0.0379

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.0878

Gnomad ASJ AF: 0.0859

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.118 AC: 17893 AN: 152110 Hom.: 1342 Cov.: 32 AF XY: 0.116 AC XY: 8650 AN XY: 74368

African (AFR) AF: 0.0378 AC: 1571 AN: 41536

American (AMR) AF: 0.0879 AC: 1342 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0859 AC: 298 AN: 3470

East Asian (EAS) AF: 0.201 AC: 1040 AN: 5164

South Asian (SAS) AF: 0.124 AC: 595 AN: 4814

European-Finnish (FIN) AF: 0.155 AC: 1637 AN: 10574

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 11027 AN: 67962

Other (OTH) AF: 0.105 AC: 222 AN: 2114

Alfa AF: 0.143 Hom.: 4864

Bravo AF: 0.108

Asia WGS AF: 0.198 AC: 686 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	3.1
DANN	Benign	0.66
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs3803833; hg19: chr17-70018911;