19-49087681-C-T

Variant names:

• chr19-49087681-C-T
• rs4802552
• NM_003089.6:c.147+1120C>T

Variant summary

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

The NM_003089.6(SNRNP70):​c.147+1120C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 152,000 control chromosomes in the GnomAD database, including 9,626 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 0.35 (9626 hom., cov: 32)
  • Exomes 𝑓: 0.42 (0 hom.)
• Consequence: SNRNP70 NM_003089.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 13 publications found

Genes affected

SNRNP70 (HGNC:11150): (small nuclear ribonucleoprotein U1 subunit 70) Enables U1 snRNA binding activity. Involved in mRNA splicing, via spliceosome and regulation of RNA splicing. Located in nucleoplasm. Part of U1 snRNP and spliceosomal complex. Implicated in disease of mental health and systemic lupus erythematosus. Biomarker of Alzheimer's disease. [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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNRNP70	NM_003089.6	c.147+1120C>T		intron_variant	Intron 2 of 9	ENST00000598441.6	NP_003080.2
SNRNP70	NM_001301069.2	c.147+1120C>T		intron_variant	Intron 2 of 9		NP_001287998.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNRNP70	ENST00000598441.6	c.147+1120C>T		intron_variant	Intron 2 of 9	1	NM_003089.6	ENSP00000472998.1

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52601 AN: 151870 Hom.: 9625 Cov.: 32

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.0751

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.356

GnomAD4 exome AF: 0.417 AC: 5 AN: 12 Hom.: 0 Cov.: 0 AF XY: 0.333 AC XY: 2 AN XY: 6

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) AF: 0.500 AC: 2 AN: 4

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.333 AC: 2 AN: 6

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.346 AC: 52616 AN: 151988 Hom.: 9626 Cov.: 32 AF XY: 0.341 AC XY: 25321 AN XY: 74276

African (AFR) AF: 0.301 AC: 12486 AN: 41458

American (AMR) AF: 0.261 AC: 3982 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1414 AN: 3460

East Asian (EAS) AF: 0.0747 AC: 387 AN: 5180

South Asian (SAS) AF: 0.459 AC: 2212 AN: 4820

European-Finnish (FIN) AF: 0.332 AC: 3506 AN: 10546

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.403 AC: 27384 AN: 67962

Other (OTH) AF: 0.353 AC: 744 AN: 2110

Alfa AF: 0.379 Hom.: 52054

Bravo AF: 0.334

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.43
DANN	Benign	0.60
PhyloP100		-1.6
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: rs4802552; hg19: chr19-49590938;