3-158376633-C-T

Variant names:

• chr3-158376633-C-T
• rs6778370
• NM_001271838.2:c.583+21725C>T

Variant summary

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

The NM_016625.4(RSRC1):​c.583+21725C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.522 in 151,942 control chromosomes in the GnomAD database, including 21,118 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 (21118 hom., cov: 31)
• Consequence: RSRC1 NM_016625.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.198
• Publications: 11 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: Ambry Genetics, Labcorp Genetics (formerly Invitae), 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016625.4. 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.583+21725C>T		intron	N/A	NP_001258767.1
	RSRC1	NM_016625.4		c.583+21725C>T		intron	N/A	NP_057709.2
	RSRC1	NM_001271834.2		c.409+21725C>T		intron	N/A	NP_001258763.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RSRC1	ENST00000611884.5	TSL:5 MANE Select	c.583+21725C>T		intron	N/A	ENSP00000481697.1
	RSRC1	ENST00000295930.7	TSL:1	c.583+21725C>T		intron	N/A	ENSP00000295930.3
	RSRC1	ENST00000312179.10	TSL:1	c.409+21725C>T		intron	N/A	ENSP00000308671.6

Frequencies

GnomAD3 genomes AF: 0.522 AC: 79287 AN: 151824 Hom.: 21094 Cov.: 31

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.522 AC: 79359 AN: 151942 Hom.: 21118 Cov.: 31 AF XY: 0.519 AC XY: 38545 AN XY: 74264

African (AFR) AF: 0.608 AC: 25200 AN: 41446

American (AMR) AF: 0.519 AC: 7922 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.473 AC: 1643 AN: 3470

East Asian (EAS) AF: 0.371 AC: 1910 AN: 5152

South Asian (SAS) AF: 0.598 AC: 2880 AN: 4820

European-Finnish (FIN) AF: 0.386 AC: 4075 AN: 10552

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.504 AC: 34254 AN: 67938

Other (OTH) AF: 0.497 AC: 1045 AN: 2102

Alfa AF: 0.519 Hom.: 14863

Bravo AF: 0.533

Asia WGS AF: 0.523 AC: 1820 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.6
DANN	Benign	0.19
PhyloP100		0.20
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: rs6778370; hg19: chr3-158094422;