chr1-167648462-A-G

Variant names:

• chr1-167648462-A-G
• rs10489193
• NM_052862.4:c.6+18033A>G

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+18033A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0992 in 152,202 control chromosomes in the GnomAD database, including 1,853 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 0.099 (1853 hom., cov: 33)
• Consequence: RCSD1 NM_052862.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.317
• 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=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RCSD1	NM_052862.4	c.6+18033A>G		intron_variant	Intron 1 of 6	ENST00000367854.8	NP_443094.3
RCSD1	NM_001322923.2	c.6+18033A>G		intron_variant	Intron 1 of 5		NP_001309852.1
RCSD1	NM_001322924.2	c.6+18033A>G		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+18033A>G		intron_variant	Intron 1 of 6	1	NM_052862.4	ENSP00000356828.3

Frequencies

GnomAD3 genomes AF: 0.0989 AC: 15047 AN: 152084 Hom.: 1842 Cov.: 33

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0759

Gnomad ASJ AF: 0.0115

Gnomad EAS AF: 0.0700

Gnomad SAS AF: 0.0685

Gnomad FIN AF: 0.0347

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00929

Gnomad OTH AF: 0.0687

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

GnomAD4 genome AF: 0.0992 AC: 15104 AN: 152202 Hom.: 1853 Cov.: 33 AF XY: 0.0993 AC XY: 7387 AN XY: 74424

African (AFR) AF: 0.291 AC: 12051 AN: 41476

American (AMR) AF: 0.0761 AC: 1164 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0115 AC: 40 AN: 3472

East Asian (EAS) AF: 0.0700 AC: 363 AN: 5186

South Asian (SAS) AF: 0.0688 AC: 332 AN: 4826

European-Finnish (FIN) AF: 0.0347 AC: 369 AN: 10622

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.00929 AC: 632 AN: 68018

Other (OTH) AF: 0.0684 AC: 144 AN: 2104

Alfa AF: 0.0340 Hom.: 1120

Bravo AF: 0.109

Asia WGS AF: 0.0920 AC: 318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	6.8
DANN	Benign	0.81
PhyloP100		0.32
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: rs10489193; hg19: chr1-167617699;