rs57440971

chr18-120296-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_033770.1(ROCK1P1):n.939-405C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0594 in 152,240 control chromosomes in the GnomAD database, including 509 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 0.059 (509 hom., cov: 32)
• Consequence: ROCK1P1 NR_033770.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.353

Genes affected

ROCK1P1 (HGNC:37832): (Rho associated coiled-coil containing protein kinase 1 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ROCK1P1	NR_033770.1	n.939-405C>T		intron_variant, non_coding_transcript_variant
ROCK1P1	NR_160777.1	n.1007-405C>T		intron_variant, non_coding_transcript_variant
ROCK1P1	NR_160778.1	n.754-405C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ROCK1P1	ENST00000608049.5	n.939-405C>T		intron_variant, non_coding_transcript_variant		1
ROCK1P1	ENST00000576266.6	n.1007-405C>T		intron_variant, non_coding_transcript_variant		4
ROCK1P1	ENST00000693583.1	n.754-405C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0594 AC: 9037 AN: 152122 Hom.: 506 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0380

Gnomad ASJ AF: 0.0865

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.00973

Gnomad FIN AF: 0.0170

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0282

Gnomad OTH AF: 0.0584

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

GnomAD4 genome AF: 0.0594 AC: 9041 AN: 152240 Hom.: 509 Cov.: 32 AF XY: 0.0575 AC XY: 4283 AN XY: 74450

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.0379

Gnomad4 ASJ AF: 0.0865

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.00974

Gnomad4 FIN AF: 0.0170

Gnomad4 NFE AF: 0.0282

Gnomad4 OTH AF: 0.0573

Alfa AF: 0.0443 Hom.: 40

Bravo AF: 0.0659

Asia WGS AF: 0.0160 AC: 57 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	8.0
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs57440971; hg19: chr18-120296;