Variant 15-40038428-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003134.6(SRP14):c.98-34G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.663 in 1,451,416 control chromosomes in the GnomAD database, including 329,760 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 0.58 ( 27389 hom., cov: 32)

Exomes 𝑓: 0.67 ( 302371 hom. )

Consequence

SRP14
NM_003134.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.276

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]

SRP14 links:

LOC124903471 (HGNC:):

LOC124903471 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.6).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.712 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
SRP14	NM_003134.6 link	c.98-34G>A	intron_variant	ENST00000267884.11	NP_003125.3	P37108
SRP14	NM_001309434.1 link	c.-87-34G>A	intron_variant		NP_001296363.1
LOC124903471	XR_007064596.1 link	n.*19C>T	downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SRP14	ENST00000267884.11 link	c.98-34G>A		intron_variant		1	NM_003134.6	ENSP00000267884.6		P37108

Frequencies

GnomAD3 genomes

AF:

0.577

AC:

87560

AN:

151856

Hom.:

27386

Cov.:

show subpopulations

Gnomad AFR

AF:

0.356

Gnomad AMI

AF:

0.816

Gnomad AMR

AF:

0.521

Gnomad ASJ

AF:

0.703

Gnomad EAS

AF:

0.267

Gnomad SAS

AF:

0.621

Gnomad FIN

AF:

0.673

Gnomad MID

AF:

0.668

Gnomad NFE

AF:

0.718

Gnomad OTH

AF:

0.604

GnomAD3 exomes

AF:

0.606

AC:

150439

AN:

248438

Hom.:

48660

AF XY:

0.620

AC XY:

83598

AN XY:

134878

show subpopulations

Gnomad AFR exome

AF:

0.345

Gnomad AMR exome

AF:

0.449

Gnomad ASJ exome

AF:

0.699

Gnomad EAS exome

AF:

0.253

Gnomad SAS exome

AF:

0.624

Gnomad FIN exome

AF:

0.684

Gnomad NFE exome

AF:

0.714

Gnomad OTH exome

AF:

0.650

GnomAD4 exome

AF:

0.673

AC:

874899

AN:

1299442

Hom.:

302371

Cov.:

AF XY:

0.674

AC XY:

441976

AN XY:

655358

show subpopulations

Gnomad4 AFR exome

AF:

0.348

Gnomad4 AMR exome

AF:

0.458

Gnomad4 ASJ exome

AF:

0.702

Gnomad4 EAS exome

AF:

0.275

Gnomad4 SAS exome

AF:

0.625

Gnomad4 FIN exome

AF:

0.683

Gnomad4 NFE exome

AF:

0.714

Gnomad4 OTH exome

AF:

0.645

GnomAD4 genome

AF:

0.576

AC:

87576

AN:

151974

Hom.:

27389

Cov.:

AF XY:

0.573

AC XY:

42534

AN XY:

74264

show subpopulations

Gnomad4 AFR

AF:

0.355

Gnomad4 AMR

AF:

0.521

Gnomad4 ASJ

AF:

0.703

Gnomad4 EAS

AF:

0.266

Gnomad4 SAS

AF:

0.622

Gnomad4 FIN

AF:

0.673

Gnomad4 NFE

AF:

0.718

Gnomad4 OTH

AF:

0.603

Alfa

AF:

0.683

Hom.:

48501

Bravo

AF:

0.551

Asia WGS

AF:

0.415

AC:

1444

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.60

CADD

Benign

DANN

Benign

0.91

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

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

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over