15-40042375-G-A

Variant names:

• chr15-40042375-G-A
• rs2412475
• ENST00000504245.9:n.201+2927G>A

Variant summary

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

The ENST00000504245.9(SRP14-DT):​n.201+2927G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 151,998 control chromosomes in the GnomAD database, including 8,817 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 0.32 (8817 hom., cov: 32)
• Consequence: SRP14-DT ENST00000504245.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.768
• Publications: 5 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000504245.9. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SRP14-DT	NR_040059.1		n.280+2785G>A		intron	N/A
	SRP14-DT	NR_040060.1		n.138+2927G>A		intron	N/A
	SRP14-DT	NR_040061.1		n.138+2927G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SRP14-DT	ENST00000504245.9	TSL:2	n.201+2927G>A		intron	N/A
	SRP14-DT	ENST00000559012.2	TSL:2	n.207+2927G>A		intron	N/A
	SRP14-DT	ENST00000560341.3	TSL:2	n.160+2927G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48494 AN: 151880 Hom.: 8796 Cov.: 32

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.320 AC: 48564 AN: 151998 Hom.: 8817 Cov.: 32 AF XY: 0.319 AC XY: 23681 AN XY: 74282

African (AFR) AF: 0.453 AC: 18768 AN: 41422

American (AMR) AF: 0.386 AC: 5902 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 691 AN: 3468

East Asian (EAS) AF: 0.567 AC: 2929 AN: 5168

South Asian (SAS) AF: 0.257 AC: 1238 AN: 4820

European-Finnish (FIN) AF: 0.251 AC: 2658 AN: 10580

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.229 AC: 15546 AN: 67950

Other (OTH) AF: 0.292 AC: 615 AN: 2108

Alfa AF: 0.336 Hom.: 4950

Bravo AF: 0.339

Asia WGS AF: 0.428 AC: 1487 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.35
DANN	Benign	0.33
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs2412475; hg19: chr15-40334576;