chr1-167682750-G-T

Variant names:

• chr1-167682750-G-T
• rs6655987
• NM_052862.4:c.7-1150G>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.7-1150G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 150,568 control chromosomes in the GnomAD database, including 4,539 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 0.23 (4539 hom., cov: 30)
• Consequence: RCSD1 NM_052862.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.174
• Publications: 0 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.43 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.7-1150G>T		intron	N/A	NP_443094.3
	RCSD1	NM_001322923.2		c.7-1150G>T		intron	N/A	NP_001309852.1
	RCSD1	NM_001322924.2		c.7-1150G>T		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.7-1150G>T		intron	N/A	ENSP00000356828.3
	RCSD1	ENST00000537350.5	TSL:1	c.7-1150G>T		intron	N/A	ENSP00000439409.1
	RCSD1	ENST00000361496.3	TSL:3	c.7-1150G>T		intron	N/A	ENSP00000355291.3

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34227 AN: 150452 Hom.: 4514 Cov.: 30

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.228 AC: 34300 AN: 150568 Hom.: 4539 Cov.: 30 AF XY: 0.233 AC XY: 17124 AN XY: 73432

African (AFR) AF: 0.329 AC: 13436 AN: 40876

American (AMR) AF: 0.254 AC: 3840 AN: 15116

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 480 AN: 3462

East Asian (EAS) AF: 0.445 AC: 2266 AN: 5088

South Asian (SAS) AF: 0.212 AC: 1009 AN: 4760

European-Finnish (FIN) AF: 0.233 AC: 2397 AN: 10272

Middle Eastern (MID) AF: 0.133 AC: 38 AN: 286

European-Non Finnish (NFE) AF: 0.152 AC: 10272 AN: 67716

Other (OTH) AF: 0.224 AC: 467 AN: 2086

Alfa AF: 0.148 Hom.: 696

Bravo AF: 0.233

Asia WGS AF: 0.338 AC: 1171 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.99
DANN	Benign	0.74
PhyloP100		-0.17
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: rs6655987; hg19: chr1-167651987;