chr5-112862289-A-T

Position:

• chr5-112862289-A-T

Variant summary

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

The NM_003135.3(SRP19):​c.42-219A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.678 in 588,038 control chromosomes in the GnomAD database, including 136,161 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 0.64 (31788 hom., cov: 31)
  • Exomes 𝑓: 0.69 (104373 hom.)
• Consequence: SRP19 NM_003135.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

Genes affected

SRP19 (HGNC:11300): (signal recognition particle 19) Enables 7S RNA binding activity. Contributes to ribosome binding activity. Predicted to be involved in SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition. Located in nucleolus. Part of signal recognition particle, endoplasmic reticulum targeting. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000258864 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SRP19	NM_003135.3	c.42-219A>T		intron_variant		ENST00000505459.6	NP_003126.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SRP19	ENST00000505459.6	c.42-219A>T		intron_variant		1	NM_003135.3	ENSP00000424870.1
ENSG00000258864	ENST00000520401.1	n.254-219A>T		intron_variant		3		ENSP00000454861.1

Frequencies

GnomAD3 genomes AF: 0.644 AC: 97745 AN: 151724 Hom.: 31780 Cov.: 31

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.701

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.656

GnomAD4 exome AF: 0.689 AC: 300595 AN: 436196 Hom.: 104373 AF XY: 0.692 AC XY: 162352 AN XY: 234526

Gnomad4 AFR exome AF: 0.556

Gnomad4 AMR exome AF: 0.740

Gnomad4 ASJ exome AF: 0.638

Gnomad4 EAS exome AF: 0.848

Gnomad4 SAS exome AF: 0.742

Gnomad4 FIN exome AF: 0.673

Gnomad4 NFE exome AF: 0.671

Gnomad4 OTH exome AF: 0.677

GnomAD4 genome AF: 0.644 AC: 97803 AN: 151842 Hom.: 31788 Cov.: 31 AF XY: 0.647 AC XY: 47997 AN XY: 74192

Gnomad4 AFR AF: 0.552

Gnomad4 AMR AF: 0.701

Gnomad4 ASJ AF: 0.614

Gnomad4 EAS AF: 0.825

Gnomad4 SAS AF: 0.757

Gnomad4 FIN AF: 0.631

Gnomad4 NFE AF: 0.668

Gnomad4 OTH AF: 0.652

Alfa AF: 0.544 Hom.: 1529

Bravo AF: 0.646

Asia WGS AF: 0.771 AC: 2680 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.4
DANN	Benign	0.38

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: rs431287; hg19: chr5-112197986;