rs4924410

chr15-40047293-A-C

Variant summary

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

The NR_040059.1(SRP14-DT):n.389+1224A>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.732 in 152,134 control chromosomes in the GnomAD database, including 41,141 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 0.73 (41141 hom., cov: 32)
• Consequence: SRP14-DT NR_040059.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93

Genes affected

SRP14-DT (HGNC:48619): (SRP14 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.965 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SRP14-DT	NR_040059.1	n.389+1224A>C		intron_variant, non_coding_transcript_variant
SRP14-DT	NR_040060.1	n.247+1224A>C		intron_variant, non_coding_transcript_variant
SRP14-DT	NR_040061.1	n.247+1224A>C		intron_variant, non_coding_transcript_variant
SRP14-DT	NR_040062.1	n.247+1224A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SRP14-DT	ENST00000692845.1	n.294+1224A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.732 AC: 111240 AN: 152014 Hom.: 41095 Cov.: 32

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.703

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.719

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.721

Gnomad OTH AF: 0.742

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.732 AC: 111338 AN: 152134 Hom.: 41141 Cov.: 32 AF XY: 0.737 AC XY: 54785 AN XY: 74364

Gnomad4 AFR AF: 0.684

Gnomad4 AMR AF: 0.823

Gnomad4 ASJ AF: 0.703

Gnomad4 EAS AF: 0.988

Gnomad4 SAS AF: 0.776

Gnomad4 FIN AF: 0.719

Gnomad4 NFE AF: 0.721

Gnomad4 OTH AF: 0.741

Alfa AF: 0.722 Hom.: 34923

Bravo AF: 0.740

Asia WGS AF: 0.862 AC: 2997 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.13
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4924410; hg19: chr15-40339494;