Variant 15-90957324-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The NM_001017919.2(RCCD1):c.378C>T(p.Ala126Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0149 in 1,542,182 control chromosomes in the GnomAD database, including 244 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.011 ( 21 hom., cov: 32)

Exomes 𝑓: 0.015 ( 223 hom. )

Consequence

RCCD1
NM_001017919.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.681

Variant links:

Genes affected

RCCD1 (HGNC:30457): (RCC1 domain containing 1) Predicted to be involved in chromatin organization. Located in cytosol and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

RCCD1 links:

RCCD1 (HGNC:):

RCCD1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.59).

BP6

Variant 15-90957324-C-T is Benign according to our data. Variant chr15-90957324-C-T is described in ClinVar as [Benign]. Clinvar id is 770436.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.681 with no splicing effect.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0112 (1702/152276) while in subpopulation NFE AF= 0.0171 (1162/68010). AF 95% confidence interval is 0.0163. There are 21 homozygotes in gnomad4. There are 743 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 21 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RCCD1	NM_001017919.2 linkuse as main transcript	c.378C>T	p.Ala126Ala	synonymous_variant	3/8	ENST00000394258.7	NP_001017919.1	A6NED2A0A024RC72

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RCCD1	ENST00000394258.7 linkuse as main transcript	c.378C>T	p.Ala126Ala	synonymous_variant	3/8	1	NM_001017919.2	ENSP00000377801.2		A6NED2

Frequencies

GnomAD3 genomes

AF:

0.0112

AC:

1703

AN:

152160

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00270

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0167

Gnomad ASJ

AF:

0.0167

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00124

Gnomad FIN

AF:

0.00650

Gnomad MID

AF:

0.00637

Gnomad NFE

AF:

0.0171

Gnomad OTH

AF:

0.0186

GnomAD3 exomes

AF:

0.00985

AC:

1401

AN:

142186

Hom.:

AF XY:

0.00986

AC XY:

751

AN XY:

76200

show subpopulations

Gnomad AFR exome

AF:

0.00160

Gnomad AMR exome

AF:

0.00808

Gnomad ASJ exome

AF:

0.0144

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00143

Gnomad FIN exome

AF:

0.00857

Gnomad NFE exome

AF:

0.0168

Gnomad OTH exome

AF:

0.0144

GnomAD4 exome

AF:

0.0153

AC:

21231

AN:

1389906

Hom.:

223

Cov.:

AF XY:

0.0149

AC XY:

10182

AN XY:

684766

show subpopulations

Gnomad4 AFR exome

AF:

0.00203

Gnomad4 AMR exome

AF:

0.00932

Gnomad4 ASJ exome

AF:

0.0128

Gnomad4 EAS exome

AF:

0.0000282

Gnomad4 SAS exome

AF:

0.00133

Gnomad4 FIN exome

AF:

0.00901

Gnomad4 NFE exome

AF:

0.0177

Gnomad4 OTH exome

AF:

0.0151

GnomAD4 genome

AF:

0.0112

AC:

1702

AN:

152276

Hom.:

Cov.:

AF XY:

0.00998

AC XY:

743

AN XY:

74462

show subpopulations

Gnomad4 AFR

AF:

0.00269

Gnomad4 AMR

AF:

0.0167

Gnomad4 ASJ

AF:

0.0167

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00124

Gnomad4 FIN

AF:

0.00650

Gnomad4 NFE

AF:

0.0171

Gnomad4 OTH

AF:

0.0184

Alfa

AF:

0.0145

Hom.:

Bravo

AF:

0.0122

Asia WGS

AF:

0.00116

AC:

AN:

3472

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Mar 29, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

7.3

DANN

Benign

0.88

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.2

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over