ENST00000504245.9:n.310+1224A>C

Variant names:

• chr15-40047293-A-C
• rs4924410
• ENST00000504245.9:n.310+1224A>C

Variant summary

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

The ENST00000504245.9(SRP14-DT):​n.310+1224A>C variant causes a intron 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 ENST00000504245.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93
• Publications: 36 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SRP14-DT	NR_040059.1	n.389+1224A>C		intron_variant	Intron 2 of 3
SRP14-DT	NR_040060.1	n.247+1224A>C		intron_variant	Intron 2 of 2
SRP14-DT	NR_040061.1	n.247+1224A>C		intron_variant	Intron 2 of 3
SRP14-DT	NR_040062.1	n.247+1224A>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SRP14-DT	ENST00000504245.9	n.310+1224A>C		intron_variant	Intron 2 of 2	2
SRP14-DT	ENST00000559012.2	n.316+1224A>C		intron_variant	Intron 2 of 6	2
SRP14-DT	ENST00000560341.3	n.269+1224A>C		intron_variant	Intron 2 of 3	2

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

African (AFR) AF: 0.684 AC: 28357 AN: 41480

American (AMR) AF: 0.823 AC: 12591 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.703 AC: 2435 AN: 3466

East Asian (EAS) AF: 0.988 AC: 5117 AN: 5180

South Asian (SAS) AF: 0.776 AC: 3744 AN: 4824

European-Finnish (FIN) AF: 0.719 AC: 7612 AN: 10580

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.721 AC: 49023 AN: 67982

Other (OTH) AF: 0.741 AC: 1566 AN: 2114

Alfa AF: 0.724 Hom.: 112735

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
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs4924410; hg19: chr15-40339494;