rs1933075

Variant names:

• chr1-167707127-C-A
• rs1933075
• NM_052862.4:c.*2431C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
RCSD1	NM_052862.4	c.*2431C>A		3_prime_UTR_variant	Exon 7 of 7	ENST00000367854.8	NP_443094.3
RCSD1	NM_001322923.2	c.*2431C>A		3_prime_UTR_variant	Exon 6 of 6		NP_001309852.1
RCSD1	NM_001322924.2	c.*2431C>A		3_prime_UTR_variant	Exon 5 of 5		NP_001309853.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RCSD1	ENST00000367854.8	c.*2431C>A		3_prime_UTR_variant	Exon 7 of 7	1	NM_052862.4	ENSP00000356828.3

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

African (AFR) AF: 0.393 AC: 16269 AN: 41424

American (AMR) AF: 0.264 AC: 4029 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 970 AN: 3470

East Asian (EAS) AF: 0.243 AC: 1257 AN: 5172

South Asian (SAS) AF: 0.296 AC: 1428 AN: 4826

European-Finnish (FIN) AF: 0.283 AC: 2977 AN: 10530

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19549 AN: 67962

Other (OTH) AF: 0.322 AC: 680 AN: 2112

Alfa AF: 0.294 Hom.: 25931

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
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs1933075; hg19: chr1-167676364;