1-167648462-A-G

Position:

• chr1-167648462-A-G

Variant summary

Our verdict is Benign. Variant got -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

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=-0.74).
• 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/exons	MANE	Protein	UniProt
RCSD1	NM_052862.4	c.6+18033A>G		intron_variant		ENST00000367854.8	NP_443094.3
RCSD1	NM_001322923.2	c.6+18033A>G		intron_variant			NP_001309852.1
RCSD1	NM_001322924.2	c.6+18033A>G		intron_variant			NP_001309853.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RCSD1	ENST00000367854.8	c.6+18033A>G		intron_variant		1	NM_052862.4	ENSP00000356828	P2
RCSD1	ENST00000537350.5	c.6+18033A>G		intron_variant		1		ENSP00000439409	A2
RCSD1	ENST00000361496.3	c.6+18033A>G		intron_variant		3		ENSP00000355291
RCSD1	ENST00000472038.1	n.170-15029A>G		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.0761

Gnomad4 ASJ AF: 0.0115

Gnomad4 EAS AF: 0.0700

Gnomad4 SAS AF: 0.0688

Gnomad4 FIN AF: 0.0347

Gnomad4 NFE AF: 0.00929

Gnomad4 OTH AF: 0.0684

Alfa AF: 0.0335 Hom.: 470

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

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: rs10489193; hg19: chr1-167617699;