3-158347120-T-C

Variant names:

• chr3-158347120-T-C
• rs827135
• NM_001271838.2:c.532-7737T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001271838.2(RSRC1):​c.532-7737T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 152,070 control chromosomes in the GnomAD database, including 13,440 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 0.41 (13440 hom., cov: 33)
• Consequence: RSRC1 NM_001271838.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RSRC1	NM_001271838.2	c.532-7737T>C		intron_variant	Intron 5 of 9	ENST00000611884.5	NP_001258767.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RSRC1	ENST00000611884.5	c.532-7737T>C		intron_variant	Intron 5 of 9	5	NM_001271838.2	ENSP00000481697.1

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62790 AN: 151954 Hom.: 13432 Cov.: 33

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.413 AC: 62830 AN: 152070 Hom.: 13440 Cov.: 33 AF XY: 0.417 AC XY: 31034 AN XY: 74346

Gnomad4 AFR AF: 0.338

Gnomad4 AMR AF: 0.432

Gnomad4 ASJ AF: 0.478

Gnomad4 EAS AF: 0.629

Gnomad4 SAS AF: 0.301

Gnomad4 FIN AF: 0.530

Gnomad4 NFE AF: 0.420

Gnomad4 OTH AF: 0.443

Alfa AF: 0.330 Hom.: 1298

Bravo AF: 0.407

Asia WGS AF: 0.419 AC: 1451 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	12
DANN	Benign	0.92

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: rs827135; hg19: chr3-158064909;