rs6441201

Variant names:

• chr3-158460535-G-A
• rs6441201
• NM_001271838.2:c.584-400G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-158460535-G-A
• chr3-158460535-G-C

Variant summary

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

The NM_001271838.2(RSRC1):​c.584-400G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 151,596 control chromosomes in the GnomAD database, including 20,139 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 0.51 (20139 hom., cov: 32)
• Consequence: RSRC1 NM_001271838.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.38
• Publications: 17 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RSRC1	NM_001271838.2	c.584-400G>A		intron_variant	Intron 6 of 9	ENST00000611884.5	NP_001258767.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RSRC1	ENST00000611884.5	c.584-400G>A		intron_variant	Intron 6 of 9	5	NM_001271838.2	ENSP00000481697.1

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76646 AN: 151478 Hom.: 20114 Cov.: 32

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.506 AC: 76720 AN: 151596 Hom.: 20139 Cov.: 32 AF XY: 0.504 AC XY: 37276 AN XY: 74028

African (AFR) AF: 0.639 AC: 26492 AN: 41444

American (AMR) AF: 0.497 AC: 7565 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1477 AN: 3460

East Asian (EAS) AF: 0.318 AC: 1643 AN: 5160

South Asian (SAS) AF: 0.600 AC: 2894 AN: 4820

European-Finnish (FIN) AF: 0.365 AC: 3847 AN: 10534

Middle Eastern (MID) AF: 0.559 AC: 162 AN: 290

European-Non Finnish (NFE) AF: 0.464 AC: 31363 AN: 67652

Other (OTH) AF: 0.487 AC: 1021 AN: 2096

Alfa AF: 0.493 Hom.: 10123

Bravo AF: 0.519

Asia WGS AF: 0.511 AC: 1770 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.3
DANN	Benign	0.59
PhyloP100		1.4
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: rs6441201; hg19: chr3-158178324;