18-136305-T-C

Variant names:

• chr18-136305-T-C
• rs7234528
• ENST00000755797.1:n.398-5176T>C

Variant summary

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

The ENST00000755797.1(ROCK1P1):​n.398-5176T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.85 in 152,130 control chromosomes in the GnomAD database, including 55,033 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 0.85 (55033 hom., cov: 32)
• Consequence: ROCK1P1 ENST00000755797.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.587
• Publications: 2 publications found

Genes affected

ROCK1P1 (HGNC:):

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 = 0.972 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
ROCK1P1	ENST00000755797.1	n.398-5176T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.849 AC: 129111 AN: 152012 Hom.: 54969 Cov.: 32

Gnomad AFR AF: 0.885

Gnomad AMI AF: 0.791

Gnomad AMR AF: 0.787

Gnomad ASJ AF: 0.832

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.805

Gnomad FIN AF: 0.885

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.830

Gnomad OTH AF: 0.847

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

GnomAD4 genome AF: 0.850 AC: 129235 AN: 152130 Hom.: 55033 Cov.: 32 AF XY: 0.850 AC XY: 63232 AN XY: 74396

African (AFR) AF: 0.886 AC: 36770 AN: 41516

American (AMR) AF: 0.788 AC: 12020 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.832 AC: 2888 AN: 3470

East Asian (EAS) AF: 0.994 AC: 5147 AN: 5176

South Asian (SAS) AF: 0.806 AC: 3877 AN: 4808

European-Finnish (FIN) AF: 0.885 AC: 9379 AN: 10594

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.830 AC: 56411 AN: 67988

Other (OTH) AF: 0.848 AC: 1795 AN: 2116

Alfa AF: 0.832 Hom.: 79130

Bravo AF: 0.848

Asia WGS AF: 0.893 AC: 3100 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.2
DANN	Benign	0.71
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs7234528; hg19: chr18-136305;