rs17398435

Positions:

• chr6-7603873-G-A
• chr6-7603873-G-C

Variant summary

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

The NM_152551.4(SNRNP48):​c.717+1129G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0535 in 152,192 control chromosomes in the GnomAD database, including 302 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 0.053 (302 hom., cov: 33)
• Consequence: SNRNP48 NM_152551.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.154

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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0787 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNRNP48	NM_152551.4	c.717+1129G>A		intron_variant		ENST00000342415.6
SNRNP48	XM_011514312.4	c.654+1129G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNRNP48	ENST00000342415.6	c.717+1129G>A		intron_variant		1	NM_152551.4	P1
SNRNP48	ENST00000634363.1	c.*275+1129G>A		intron_variant, NMD_transcript_variant		2
SNRNP48	ENST00000496946.1	n.1974+1129G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0535 AC: 8139 AN: 152074 Hom.: 302 Cov.: 33

Gnomad AFR AF: 0.0131

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.0490

Gnomad ASJ AF: 0.0547

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.0451

Gnomad FIN AF: 0.0699

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0805

Gnomad OTH AF: 0.0497

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

GnomAD4 genome AF: 0.0535 AC: 8142 AN: 152192 Hom.: 302 Cov.: 33 AF XY: 0.0523 AC XY: 3893 AN XY: 74420

Gnomad4 AFR AF: 0.0131

Gnomad4 AMR AF: 0.0489

Gnomad4 ASJ AF: 0.0547

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0462

Gnomad4 FIN AF: 0.0699

Gnomad4 NFE AF: 0.0805

Gnomad4 OTH AF: 0.0492

Alfa AF: 0.0646 Hom.: 239

Bravo AF: 0.0507

Asia WGS AF: 0.0130 AC: 47 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	11
DANN	Benign	0.82

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: rs17398435; hg19: chr6-7604106;