chr15-40068540-A-G

Position:

• chr15-40068540-A-G

Variant summary

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

The ENST00000692845.1(SRP14-DT):​n.295-5213A>G 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 0.312 in 150,686 control chromosomes in the GnomAD database, including 7,558 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 0.31 (7558 hom., cov: 30)
• Consequence: SRP14-DT ENST00000692845.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.758

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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SRP14-DT	ENST00000692845.1	n.295-5213A>G		intron_variant, non_coding_transcript_variant
SRP14-DT	ENST00000655221.1	n.295-5213A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.312 AC: 46994 AN: 150574 Hom.: 7552 Cov.: 30

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.368

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.312 AC: 47019 AN: 150686 Hom.: 7558 Cov.: 30 AF XY: 0.309 AC XY: 22727 AN XY: 73464

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.337

Gnomad4 OTH AF: 0.305

Alfa AF: 0.328 Hom.: 16119

Bravo AF: 0.301

Asia WGS AF: 0.272 AC: 943 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.22
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7181230; hg19: chr15-40360741;