6-7603873-G-A

Variant names:

• chr6-7603873-G-A
• rs17398435
• NM_152551.4:c.717+1129G>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.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
• Publications: 4 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0787 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.717+1129G>A		intron	N/A	NP_689764.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNRNP48	ENST00000342415.6	TSL:1 MANE Select	c.717+1129G>A		intron	N/A	ENSP00000339834.4
	SNRNP48	ENST00000496946.1	TSL:2	n.1974+1129G>A		intron	N/A
	SNRNP48	ENST00000634363.1	TSL:2	n.*275+1129G>A		intron	N/A	ENSP00000489245.1

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

African (AFR) AF: 0.0131 AC: 543 AN: 41534

American (AMR) AF: 0.0489 AC: 748 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0547 AC: 190 AN: 3472

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5178

South Asian (SAS) AF: 0.0462 AC: 223 AN: 4830

European-Finnish (FIN) AF: 0.0699 AC: 739 AN: 10570

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0805 AC: 5472 AN: 68004

Other (OTH) AF: 0.0492 AC: 104 AN: 2114

Alfa AF: 0.0578 Hom.: 361

Bravo AF: 0.0507

Asia WGS AF: 0.0130 AC: 47 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	11
DANN	Benign	0.82
PhyloP100		0.15
Mutation Taster		=99/1	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: rs17398435; hg19: chr6-7604106;