rs2757598

Variant names:

• chr6-7609803-C-A
• rs2757598
• NM_152551.4:c.*930C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-7609803-C-A
• chr6-7609803-C-G
• chr6-7609803-C-T

Variant summary

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

The NM_152551.4(SNRNP48):​c.*930C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.696 in 151,988 control chromosomes in the GnomAD database, including 37,282 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 0.70 (37282 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: SNRNP48 NM_152551.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270
• Publications: 5 publications found

Genes affected

SNRNP48 (HGNC:21368): (small nuclear ribonucleoprotein U11/U12 subunit 48) Predicted to enable metal ion binding activity. Predicted to be involved in RNA splicing. Located in cytosol and nucleoplasm. Part of U12-type spliceosomal complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.809 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152551.4. 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
	SNRNP48	NM_152551.4	MANE Select	c.*930C>A		3_prime_UTR	Exon 9 of 9	NP_689764.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNRNP48	ENST00000342415.6	TSL:1 MANE Select	c.*930C>A		3_prime_UTR	Exon 9 of 9	ENSP00000339834.4

Frequencies

GnomAD3 genomes AF: 0.696 AC: 105693 AN: 151872 Hom.: 37224 Cov.: 31

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.757

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.683

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.696 AC: 105800 AN: 151988 Hom.: 37282 Cov.: 31 AF XY: 0.696 AC XY: 51678 AN XY: 74292

African (AFR) AF: 0.816 AC: 33826 AN: 41430

American (AMR) AF: 0.695 AC: 10608 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.757 AC: 2622 AN: 3464

East Asian (EAS) AF: 0.604 AC: 3119 AN: 5160

South Asian (SAS) AF: 0.663 AC: 3190 AN: 4810

European-Finnish (FIN) AF: 0.666 AC: 7039 AN: 10568

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.635 AC: 43139 AN: 67980

Other (OTH) AF: 0.686 AC: 1441 AN: 2100

Alfa AF: 0.653 Hom.: 123807

Bravo AF: 0.701

Asia WGS AF: 0.669 AC: 2331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.8
DANN	Benign	0.49
PhyloP100		0.027
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: rs2757598; hg19: chr6-7610036; COSMIC: COSV60938853; COSMIC: COSV60938853;