Variant chr11-67066781-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_014578.4(RHOD):c.264C>T(p.Asp88=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.368 in 1,611,384 control chromosomes in the GnomAD database, including 114,190 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 0.33 ( 9132 hom., cov: 33)

Exomes 𝑓: 0.37 ( 105058 hom. )

Consequence

RHOD
NM_014578.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.57

Variant links:

Genes affected

RHOD (HGNC:670): (ras homolog family member D) Ras homolog, or Rho, proteins interact with protein kinases and may serve as targets for activated GTPase. They play a critical role in muscle differentiation. The protein encoded by this gene binds GTP and is a member of the small GTPase superfamily. It is involved in endosome dynamics and reorganization of the actin cytoskeleton, and it may coordinate membrane transport with the function of the cytoskeleton. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2014]

RHOD links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP7

Synonymous conserved (PhyloP=-4.57 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RHOD	NM_014578.4 linkuse as main transcript	c.264C>T	p.Asp88=	synonymous_variant	3/5	ENST00000308831.7
RHOD	NM_001300886.2 linkuse as main transcript	c.133-3644C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
RHOD	ENST00000308831.7 linkuse as main transcript	c.264C>T	p.Asp88=	synonymous_variant	3/5	1	NM_014578.4	P1
RHOD	ENST00000532559.1 linkuse as main transcript	c.133-3644C>T		intron_variant		3
RHOD	ENST00000533360.2 linkuse as main transcript	n.307C>T		non_coding_transcript_exon_variant	3/4	2

Frequencies

GnomAD3 genomes

AF:

0.329

AC:

50052

AN:

152074

Hom.:

9135

Cov.:

show subpopulations

Gnomad AFR

AF:

0.188

Gnomad AMI

AF:

0.405

Gnomad AMR

AF:

0.481

Gnomad ASJ

AF:

0.419

Gnomad EAS

AF:

0.463

Gnomad SAS

AF:

0.515

Gnomad FIN

AF:

0.276

Gnomad MID

AF:

0.373

Gnomad NFE

AF:

0.359

Gnomad OTH

AF:

0.356

GnomAD3 exomes

AF:

0.400

AC:

100562

AN:

251390

Hom.:

21849

AF XY:

0.398

AC XY:

54103

AN XY:

135866

show subpopulations

Gnomad AFR exome

AF:

0.183

Gnomad AMR exome

AF:

0.597

Gnomad ASJ exome

AF:

0.405

Gnomad EAS exome

AF:

0.457

Gnomad SAS exome

AF:

0.498

Gnomad FIN exome

AF:

0.277

Gnomad NFE exome

AF:

0.359

Gnomad OTH exome

AF:

0.390

GnomAD4 exome

AF:

0.372

AC:

543073

AN:

1459192

Hom.:

105058

Cov.:

AF XY:

0.375

AC XY:

271909

AN XY:

725998

show subpopulations

Gnomad4 AFR exome

AF:

0.179

Gnomad4 AMR exome

AF:

0.587

Gnomad4 ASJ exome

AF:

0.411

Gnomad4 EAS exome

AF:

0.466

Gnomad4 SAS exome

AF:

0.494

Gnomad4 FIN exome

AF:

0.282

Gnomad4 NFE exome

AF:

0.359

Gnomad4 OTH exome

AF:

0.378

GnomAD4 genome

AF:

0.329

AC:

50060

AN:

152192

Hom.:

9132

Cov.:

AF XY:

0.332

AC XY:

24727

AN XY:

74432

show subpopulations

Gnomad4 AFR

AF:

0.188

Gnomad4 AMR

AF:

0.481

Gnomad4 ASJ

AF:

0.419

Gnomad4 EAS

AF:

0.464

Gnomad4 SAS

AF:

0.515

Gnomad4 FIN

AF:

0.276

Gnomad4 NFE

AF:

0.359

Gnomad4 OTH

AF:

0.360

Alfa

AF:

0.344

Hom.:

4817

Bravo

AF:

0.340

Asia WGS

AF:

0.441

AC:

1536

AN:

3478

EpiCase

AF:

0.365

EpiControl

AF:

0.368

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.48

DANN

Benign

0.35

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over