rs761076

chr1-167650745-C-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.91).
• 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/exons	MANE	UniProt
RCSD1	NM_052862.4	c.6+20316C>T		intron_variant		ENST00000367854.8
RCSD1	NM_001322923.2	c.6+20316C>T		intron_variant
RCSD1	NM_001322924.2	c.6+20316C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RCSD1	ENST00000367854.8	c.6+20316C>T		intron_variant		1	NM_052862.4	P2
RCSD1	ENST00000537350.5	c.6+20316C>T		intron_variant		1		A2
RCSD1	ENST00000361496.3	c.6+20316C>T		intron_variant		3
RCSD1	ENST00000472038.1	n.170-12746C>T		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.482

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.486

Gnomad4 EAS AF: 0.571

Gnomad4 SAS AF: 0.464

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.437

Gnomad4 OTH AF: 0.480

Alfa AF: 0.438 Hom.: 8497

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

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: rs761076; hg19: chr1-167619982;