rs749130159

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

The NM_003134.6(SRP14):​c.370_381delCCAACAACAGCA​(p.Pro124_Ala127del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00337 in 1,613,534 control chromosomes in the GnomAD database, including 27 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0033 ( 2 hom., cov: 33)
Exomes 𝑓: 0.0034 ( 25 hom. )

Consequence

SRP14
NM_003134.6 conservative_inframe_deletion

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.33
Variant links:
Genes affected
SRP14 (HGNC:11299): (signal recognition particle 14) Enables RNA binding activity. Involved in protein targeting to ER. Located in nucleus. Part of signal recognition particle, endoplasmic reticulum targeting. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6
Variant 15-40036362-CTGCTGTTGTTGG-C is Benign according to our data. Variant chr15-40036362-CTGCTGTTGTTGG-C is described in ClinVar as [Likely_benign]. Clinvar id is 2645164.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00338 (4941/1461342) while in subpopulation MID AF= 0.0342 (197/5766). AF 95% confidence interval is 0.0303. There are 25 homozygotes in gnomad4_exome. There are 2551 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.
BS2
High AC in GnomAd4 at 503 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SRP14NM_003134.6 linkc.370_381delCCAACAACAGCA p.Pro124_Ala127del conservative_inframe_deletion Exon 5 of 5 ENST00000267884.11 NP_003125.3 P37108
SRP14NM_001309434.1 linkc.226_237delCCAACAACAGCA p.Pro76_Ala79del conservative_inframe_deletion Exon 6 of 6 NP_001296363.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SRP14ENST00000267884.11 linkc.370_381delCCAACAACAGCA p.Pro124_Ala127del conservative_inframe_deletion Exon 5 of 5 1 NM_003134.6 ENSP00000267884.6 P37108

Frequencies

GnomAD3 genomes
AF:
0.00331
AC:
504
AN:
152074
Hom.:
2
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00295
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00517
Gnomad ASJ
AF:
0.0118
Gnomad EAS
AF:
0.000970
Gnomad SAS
AF:
0.00394
Gnomad FIN
AF:
0.000943
Gnomad MID
AF:
0.0253
Gnomad NFE
AF:
0.00303
Gnomad OTH
AF:
0.00672
GnomAD3 exomes
AF:
0.00368
AC:
925
AN:
251264
Hom.:
5
AF XY:
0.00386
AC XY:
524
AN XY:
135842
show subpopulations
Gnomad AFR exome
AF:
0.00303
Gnomad AMR exome
AF:
0.00330
Gnomad ASJ exome
AF:
0.0174
Gnomad EAS exome
AF:
0.000762
Gnomad SAS exome
AF:
0.00350
Gnomad FIN exome
AF:
0.00139
Gnomad NFE exome
AF:
0.00362
Gnomad OTH exome
AF:
0.00408
GnomAD4 exome
AF:
0.00338
AC:
4941
AN:
1461342
Hom.:
25
AF XY:
0.00351
AC XY:
2551
AN XY:
726968
show subpopulations
Gnomad4 AFR exome
AF:
0.00323
Gnomad4 AMR exome
AF:
0.00300
Gnomad4 ASJ exome
AF:
0.0171
Gnomad4 EAS exome
AF:
0.000630
Gnomad4 SAS exome
AF:
0.00382
Gnomad4 FIN exome
AF:
0.00157
Gnomad4 NFE exome
AF:
0.00302
Gnomad4 OTH exome
AF:
0.00427
GnomAD4 genome
AF:
0.00331
AC:
503
AN:
152192
Hom.:
2
Cov.:
33
AF XY:
0.00351
AC XY:
261
AN XY:
74410
show subpopulations
Gnomad4 AFR
AF:
0.00294
Gnomad4 AMR
AF:
0.00517
Gnomad4 ASJ
AF:
0.0118
Gnomad4 EAS
AF:
0.000972
Gnomad4 SAS
AF:
0.00374
Gnomad4 FIN
AF:
0.000943
Gnomad4 NFE
AF:
0.00303
Gnomad4 OTH
AF:
0.00665
Alfa
AF:
0.00373
Hom.:
0

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Mar 01, 2023
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

SRP14: BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs749130159; hg19: chr15-40328563; API