chr1-167640713-G-A

Variant names:

• chr1-167640713-G-A
• rs1890128
• NM_052862.4:c.6+10284G>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.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
• Publications: 3 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.06 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_052862.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RCSD1	NM_052862.4	MANE Select	c.6+10284G>A		intron	N/A	NP_443094.3
	RCSD1	NM_001322923.2		c.6+10284G>A		intron	N/A	NP_001309852.1
	RCSD1	NM_001322924.2		c.6+10284G>A		intron	N/A	NP_001309853.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RCSD1	ENST00000367854.8	TSL:1 MANE Select	c.6+10284G>A		intron	N/A	ENSP00000356828.3
	RCSD1	ENST00000537350.5	TSL:1	c.6+10284G>A		intron	N/A	ENSP00000439409.1
	RCSD1	ENST00000361496.3	TSL:3	c.6+10284G>A		intron	N/A	ENSP00000355291.3

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

African (AFR) AF: 0.00 AC: 0 AN: 10

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 12

South Asian (SAS) AF: 0.00 AC: 0 AN: 6

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.0301 AC: 5 AN: 166

Other (OTH) AF: 0.00 AC: 0 AN: 10

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

African (AFR) AF: 0.0620 AC: 2568 AN: 41420

American (AMR) AF: 0.0245 AC: 374 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0476 AC: 165 AN: 3464

East Asian (EAS) AF: 0.00 AC: 0 AN: 5160

South Asian (SAS) AF: 0.00187 AC: 9 AN: 4808

European-Finnish (FIN) AF: 0.0240 AC: 254 AN: 10604

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0368 AC: 2499 AN: 67948

Other (OTH) AF: 0.0369 AC: 78 AN: 2112

Alfa AF: 0.0441 Hom.: 19

Bravo AF: 0.0405

Asia WGS AF: 0.00664 AC: 23 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.93
DANN	Benign	0.51
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism

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: rs1890128; hg19: chr1-167609950;