rs1890128

chr1-167640713-G-A

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RCSD1	NM_052862.4	c.6+10284G>A		intron_variant		ENST00000367854.8
RCSD1	NM_001322923.2	c.6+10284G>A		intron_variant
RCSD1	NM_001322924.2	c.6+10284G>A		intron_variant
RCSD1	NR_136519.2	n.340+1G>A		splice_donor_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RCSD1	ENST00000367854.8	c.6+10284G>A		intron_variant		1	NM_052862.4	P2

Frequencies

GnomAD3 genomes AF: 0.0392 AC: 5959 AN: 151882 Hom.: 146 Cov.: 32

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: 5 AN: 214 Hom.: 0 Cov.: 0 AF XY: 0.0253 AC XY: 4 AN XY: 158

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0301

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0393 AC: 5969 AN: 152000 Hom.: 146 Cov.: 32 AF XY: 0.0372 AC XY: 2762 AN XY: 74306

Gnomad4 AFR AF: 0.0620

Gnomad4 AMR AF: 0.0245

Gnomad4 ASJ AF: 0.0476

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00187

Gnomad4 FIN AF: 0.0240

Gnomad4 NFE AF: 0.0368

Gnomad4 OTH AF: 0.0369

Alfa AF: 0.0430 Hom.: 18

Bravo AF: 0.0405

Asia WGS AF: 0.00664 AC: 23 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.93
Dann	Benign	0.51

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

Other links and lift over

dbSNP: rs1890128; hg19: chr1-167609950;