rs4510417

Variant names:

• chr3-158491764-T-A
• rs4510417
• NM_001271838.2:c.652+30761T>A

Your query was ambiguous. Multiple possible variants found:

• chr3-158491764-T-A
• chr3-158491764-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001271838.2(RSRC1):​c.652+30761T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.52 in 151,980 control chromosomes in the GnomAD database, including 21,128 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 0.52 (21128 hom., cov: 32)
• Consequence: RSRC1 NM_001271838.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86
• Publications: 3 publications found

Genes affected

RSRC1 (HGNC:24152): (arginine and serine rich coiled-coil 1) This gene encodes a member of the serine and arginine rich-related protein family. The encoded protein is involved in both constitutive and alternative mRNA splicing. This gene may be associated with schizophrenia. A pseudogene of this gene is located on chromosome 9. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Nov 2012]

RSRC1 Gene-Disease associations (from GenCC):

• intellectual developmental disorder, autosomal recessive 70

  Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), PanelApp Australia, Ambry Genetics, G2P
• autosomal recessive non-syndromic intellectual disability

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

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 (AFR) allele frequency at 95% confidence interval = 0.635 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001271838.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RSRC1	NM_001271838.2	MANE Select	c.652+30761T>A		intron	N/A	NP_001258767.1	Q96IZ7-1
	RSRC1	NM_016625.4		c.652+30761T>A		intron	N/A	NP_057709.2
	RSRC1	NM_001271834.2		c.478+30761T>A		intron	N/A	NP_001258763.1	Q96IZ7-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RSRC1	ENST00000611884.5	TSL:5 MANE Select	c.652+30761T>A		intron	N/A	ENSP00000481697.1	Q96IZ7-1
	RSRC1	ENST00000295930.7	TSL:1	c.652+30761T>A		intron	N/A	ENSP00000295930.3	Q96IZ7-1
	RSRC1	ENST00000312179.10	TSL:1	c.478+30761T>A		intron	N/A	ENSP00000308671.6	Q96IZ7-2

Frequencies

GnomAD3 genomes AF: 0.520 AC: 79017 AN: 151862 Hom.: 21105 Cov.: 32

Gnomad AFR AF: 0.641

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.520 AC: 79088 AN: 151980 Hom.: 21128 Cov.: 32 AF XY: 0.521 AC XY: 38684 AN XY: 74280

African (AFR) AF: 0.641 AC: 26579 AN: 41446

American (AMR) AF: 0.512 AC: 7819 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1484 AN: 3472

East Asian (EAS) AF: 0.326 AC: 1689 AN: 5174

South Asian (SAS) AF: 0.605 AC: 2916 AN: 4820

European-Finnish (FIN) AF: 0.426 AC: 4492 AN: 10550

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.479 AC: 32558 AN: 67934

Other (OTH) AF: 0.494 AC: 1041 AN: 2108

Alfa AF: 0.505 Hom.: 2464

Bravo AF: 0.529

Asia WGS AF: 0.516 AC: 1789 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.17
DANN	Benign	0.71
PhyloP100		-1.9
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: rs4510417; hg19: chr3-158209553;