3-158276049-G-T

Variant names:

• chr3-158276049-G-T
• rs2682405
• NM_001271838.2:c.495-21990G>T

Variant summary

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

The NM_001271838.2(RSRC1):​c.495-21990G>T variant causes a intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.409 in 845,602 control chromosomes in the GnomAD database, including 75,339 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 0.48 (17791 hom., cov: 32)
  • Exomes 𝑓: 0.39 (57548 hom.)
• Consequence: RSRC1 NM_001271838.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.25
• Publications: 6 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]

RPL15P6 (HGNC:36185): (ribosomal protein L15 pseudogene 6)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.625 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RSRC1	NM_001271838.2	MANE Select	c.495-21990G>T		intron	N/A	NP_001258767.1
	RSRC1	NM_016625.4		c.495-21990G>T		intron	N/A	NP_057709.2
	RSRC1	NM_001271834.2		c.321-21990G>T		intron	N/A	NP_001258763.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RSRC1	ENST00000611884.5	TSL:5 MANE Select	c.495-21990G>T		intron	N/A	ENSP00000481697.1
	RSRC1	ENST00000295930.7	TSL:1	c.495-21990G>T		intron	N/A	ENSP00000295930.3
	RSRC1	ENST00000312179.10	TSL:1	c.321-21990G>T		intron	N/A	ENSP00000308671.6

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72298 AN: 151760 Hom.: 17769 Cov.: 32

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.643

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.496

GnomAD4 exome AF: 0.395 AC: 273692 AN: 693726 Hom.: 57548 Cov.: 9 AF XY: 0.391 AC XY: 145772 AN XY: 372952

African (AFR) AF: 0.531 AC: 9762 AN: 18400

American (AMR) AF: 0.421 AC: 18131 AN: 43052

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 9430 AN: 20808

East Asian (EAS) AF: 0.616 AC: 21101 AN: 34262

South Asian (SAS) AF: 0.286 AC: 20551 AN: 71928

European-Finnish (FIN) AF: 0.504 AC: 18561 AN: 36826

Middle Eastern (MID) AF: 0.381 AC: 992 AN: 2606

European-Non Finnish (NFE) AF: 0.373 AC: 160805 AN: 431124

Other (OTH) AF: 0.414 AC: 14359 AN: 34720

GnomAD4 genome AF: 0.476 AC: 72367 AN: 151876 Hom.: 17791 Cov.: 32 AF XY: 0.479 AC XY: 35548 AN XY: 74212

African (AFR) AF: 0.559 AC: 23150 AN: 41412

American (AMR) AF: 0.447 AC: 6821 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1656 AN: 3468

East Asian (EAS) AF: 0.644 AC: 3310 AN: 5142

South Asian (SAS) AF: 0.300 AC: 1442 AN: 4808

European-Finnish (FIN) AF: 0.531 AC: 5594 AN: 10532

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.421 AC: 28630 AN: 67940

Other (OTH) AF: 0.494 AC: 1041 AN: 2106

Alfa AF: 0.438 Hom.: 19869

Bravo AF: 0.479

Asia WGS AF: 0.442 AC: 1539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	2.5
DANN	Benign	0.71
PhyloP100		7.2
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: rs2682405; hg19: chr3-157993838; COSMIC: COSV55829781;