dbSNP rs1890128: RCSD1:c.6+10284G>A (chr1-167640713-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_052862.4(RCSD1):c.6+10284G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0392 in 152,214 control chromosomes in the GnomAD database, including 146 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 0.039 ( 146 hom., cov: 32)

Exomes 𝑓: 0.023 ( 0 hom. )

Consequence

RCSD1
NM_052862.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.48

Publications

3 publications found

Variant links:

Genes affected

RCSD1 (HGNC:28310): (RCSD domain containing 1) Enables actin filament binding activity. Involved in cellular hyperosmotic response. Predicted to be located in actin filament. [provided by Alliance of Genome Resources, Apr 2022]

RCSD1 links:

ENSG00000241666 (HGNC:):

ENSG00000241666 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.06 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_052862.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
RCSD1	NM_052862.4	MANE Select	c.6+10284G>A	intron	N/A	NP_443094.3
RCSD1	NM_001322923.2		c.6+10284G>A	intron	N/A	NP_001309852.1	B7ZKW8
RCSD1	NM_001322924.2		c.6+10284G>A	intron	N/A	NP_001309853.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
RCSD1	ENST00000367854.8	TSL:1 MANE Select	c.6+10284G>A	intron	N/A	ENSP00000356828.3	Q6JBY9-1
RCSD1	ENST00000537350.5	TSL:1	c.6+10284G>A	intron	N/A	ENSP00000439409.1	B7ZKW8
RCSD1	ENST00000900257.1		c.6+10284G>A	intron	N/A	ENSP00000570316.1

Frequencies

GnomAD3 genomes

AF:

0.0392

AC:

5959

AN:

151882

Hom.:

146

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0619

Gnomad AMI

AF:

0.0175

Gnomad AMR

AF:

0.0245

Gnomad ASJ

AF:

0.0476

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00187

Gnomad FIN

AF:

0.0240

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.0368

Gnomad OTH

AF:

0.0373

GnomAD4 exome

AF:

0.0234

AC:

AN:

214

Hom.:

Cov.:

AF XY:

0.0253

AC XY:

AN XY:

158

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0301

AC:

AN:

166

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0393

AC:

5969

AN:

152000

Hom.:

146

Cov.:

AF XY:

0.0372

AC XY:

2762

AN XY:

74306

show subpopulations

African (AFR)

AF:

0.0620

AC:

2568

AN:

41420

American (AMR)

AF:

0.0245

AC:

374

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.0476

AC:

165

AN:

3464

East Asian (EAS)

AF:

0.00

AC:

AN:

5160

South Asian (SAS)

AF:

0.00187

AC:

AN:

4808

European-Finnish (FIN)

AF:

0.0240

AC:

254

AN:

10604

Middle Eastern (MID)

AF:

0.0204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0368

AC:

2499

AN:

67948

Other (OTH)

AF:

0.0369

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

284

568

852

1136

1420

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

140

210

280

350

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0441

Hom.:

Bravo

AF:

0.0405

Asia WGS

AF:

0.00664

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.93

(source)

DANN

Benign

0.51

PhyloP100

-1.5

Mutation Taster

=100/0

polymorphism

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over