NM_152551.4:c.*1380G>A

Variant names:

• chr6-7610253-G-A
• rs2806218
• NM_152551.4:c.*1380G>A

Variant summary

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

The NM_152551.4(SNRNP48):​c.*1380G>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 0.699 in 152,108 control chromosomes in the GnomAD database, including 37,603 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 (37603 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: SNRNP48 NM_152551.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.826
• 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNRNP48	NM_152551.4	c.*1380G>A		3_prime_UTR_variant	Exon 9 of 9	ENST00000342415.6	NP_689764.3
SNRNP48	XM_011514312.4	c.*1380G>A		3_prime_UTR_variant	Exon 9 of 9		XP_011512614.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNRNP48	ENST00000342415.6	c.*1380G>A		3_prime_UTR_variant	Exon 9 of 9	1	NM_152551.4	ENSP00000339834.4

Frequencies

GnomAD3 genomes AF: 0.698 AC: 106142 AN: 151992 Hom.: 37544 Cov.: 33

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.755

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: 0.684

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: 0.699 AC: 106250 AN: 152108 Hom.: 37603 Cov.: 33 AF XY: 0.698 AC XY: 51883 AN XY: 74332

African (AFR) AF: 0.824 AC: 34230 AN: 41518

American (AMR) AF: 0.695 AC: 10622 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.755 AC: 2619 AN: 3470

East Asian (EAS) AF: 0.604 AC: 3127 AN: 5174

South Asian (SAS) AF: 0.663 AC: 3195 AN: 4816

European-Finnish (FIN) AF: 0.666 AC: 7036 AN: 10558

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

European-Non Finnish (NFE) AF: 0.635 AC: 43155 AN: 67980

Other (OTH) AF: 0.687 AC: 1451 AN: 2112

Alfa AF: 0.658 Hom.: 42155

Bravo AF: 0.704

Asia WGS AF: 0.670 AC: 2332 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.0
DANN	Benign	0.24
PhyloP100		-0.83
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: rs2806218; hg19: chr6-7610486;