rs2412475

Positions:

• chr15-40042375-G-A

Variant summary

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

The NR_040059.1(SRP14-DT):​n.280+2785G>A 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 0.32 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 NR_040059.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.768

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SRP14-DT	NR_040059.1	n.280+2785G>A		intron_variant, non_coding_transcript_variant
SRP14-DT	NR_040060.1	n.138+2927G>A		intron_variant, non_coding_transcript_variant
SRP14-DT	NR_040061.1	n.138+2927G>A		intron_variant, non_coding_transcript_variant
SRP14-DT	NR_040062.1	n.138+2927G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SRP14-DT	ENST00000692845.1	n.185+2927G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.453

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.567

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.292

Alfa AF: 0.307 Hom.: 1627

Bravo AF: 0.339

Asia WGS AF: 0.428 AC: 1487 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2412475; hg19: chr15-40334576;