NM_052862.4:c.6+20316C>T

Variant names:

• chr1-167650745-C-T
• rs761076
• NM_052862.4:c.6+20316C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_052862.4(RCSD1):​c.6+20316C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 151,882 control chromosomes in the GnomAD database, including 15,561 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 0.45 (15561 hom., cov: 31)
• Consequence: RCSD1 NM_052862.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 2 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]

ENSG00000241666 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RCSD1	NM_052862.4	c.6+20316C>T		intron_variant	Intron 1 of 6	ENST00000367854.8	NP_443094.3
RCSD1	NM_001322923.2	c.6+20316C>T		intron_variant	Intron 1 of 5		NP_001309852.1
RCSD1	NM_001322924.2	c.6+20316C>T		intron_variant	Intron 1 of 4		NP_001309853.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RCSD1	ENST00000367854.8	c.6+20316C>T		intron_variant	Intron 1 of 6	1	NM_052862.4	ENSP00000356828.3

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68257 AN: 151764 Hom.: 15546 Cov.: 31

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.570

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.450 AC: 68302 AN: 151882 Hom.: 15561 Cov.: 31 AF XY: 0.447 AC XY: 33197 AN XY: 74224

African (AFR) AF: 0.482 AC: 19942 AN: 41396

American (AMR) AF: 0.424 AC: 6475 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1689 AN: 3472

East Asian (EAS) AF: 0.571 AC: 2938 AN: 5148

South Asian (SAS) AF: 0.464 AC: 2231 AN: 4810

European-Finnish (FIN) AF: 0.368 AC: 3874 AN: 10538

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.437 AC: 29681 AN: 67930

Other (OTH) AF: 0.480 AC: 1010 AN: 2106

Alfa AF: 0.438 Hom.: 11282

Bravo AF: 0.456

Asia WGS AF: 0.505 AC: 1756 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.16
DANN	Benign	0.76
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs761076; hg19: chr1-167619982;