rs1539537

Positions:

• chr6-7609283-T-C

Variant summary

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

The NM_152551.4(SNRNP48):​c.*410T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.706 in 152,602 control chromosomes in the GnomAD database, including 38,666 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 0.71 (38514 hom., cov: 32)
  • Exomes 𝑓: 0.72 (152 hom.)
• Consequence: SNRNP48 NM_152551.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.351

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.841 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SNRNP48	NM_152551.4	c.*410T>C		3_prime_UTR_variant	9/9	ENST00000342415.6	NP_689764.3
SNRNP48	XM_011514312.4	c.*410T>C		3_prime_UTR_variant	9/9		XP_011512614.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SNRNP48	ENST00000342415.6	c.*410T>C		3_prime_UTR_variant	9/9	1	NM_152551.4	ENSP00000339834.4

Frequencies

GnomAD3 genomes AF: 0.706 AC: 107219 AN: 151932 Hom.: 38452 Cov.: 32

Gnomad AFR AF: 0.848

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.756

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.688

GnomAD4 exome AF: 0.723 AC: 399 AN: 552 Hom.: 152 Cov.: 0 AF XY: 0.719 AC XY: 220 AN XY: 306

Gnomad4 AFR exome AF: 0.833

Gnomad4 AMR exome AF: 0.636

Gnomad4 ASJ exome AF: 0.864

Gnomad4 EAS exome AF: 0.750

Gnomad4 SAS exome AF: 0.750

Gnomad4 FIN exome AF: 0.976

Gnomad4 NFE exome AF: 0.616

Gnomad4 OTH exome AF: 0.818

GnomAD4 genome AF: 0.706 AC: 107331 AN: 152050 Hom.: 38514 Cov.: 32 AF XY: 0.705 AC XY: 52404 AN XY: 74320

Gnomad4 AFR AF: 0.848

Gnomad4 AMR AF: 0.698

Gnomad4 ASJ AF: 0.756

Gnomad4 EAS AF: 0.607

Gnomad4 SAS AF: 0.665

Gnomad4 FIN AF: 0.666

Gnomad4 NFE AF: 0.636

Gnomad4 OTH AF: 0.691

Alfa AF: 0.670 Hom.: 10824

Bravo AF: 0.712

Asia WGS AF: 0.673 AC: 2342 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.37
DANN	Benign	0.40

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: rs1539537; hg19: chr6-7609516;