rs1933075

chr1-167707127-C-A

Variant summary

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

The NM_052862.4(RCSD1):c.*2431C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 151,972 control chromosomes in the GnomAD database, including 7,663 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 0.31 (7663 hom., cov: 32)
• Consequence: RCSD1 NM_052862.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.09

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=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RCSD1	NM_052862.4	c.*2431C>A		3_prime_UTR_variant	7/7	ENST00000367854.8
RCSD1	NM_001322923.2	c.*2431C>A		3_prime_UTR_variant	6/6
RCSD1	NM_001322924.2	c.*2431C>A		3_prime_UTR_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RCSD1	ENST00000367854.8	c.*2431C>A		3_prime_UTR_variant	7/7	1	NM_052862.4	P2

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47320 AN: 151852 Hom.: 7646 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.312 AC: 47388 AN: 151972 Hom.: 7663 Cov.: 32 AF XY: 0.308 AC XY: 22909 AN XY: 74272

Gnomad4 AFR AF: 0.393

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.280

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.296

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.322

Alfa AF: 0.291 Hom.: 10933

Bravo AF: 0.313

Asia WGS AF: 0.281 AC: 983 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	9.1
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1933075; hg19: chr1-167676364;