rs3923235

Positions:

• chr15-40078920-A-G

Variant summary

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

The ENST00000616620.1(ENSG00000275636):​n.29A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 152,184 control chromosomes in the GnomAD database, including 5,464 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 0.26 (5464 hom., cov: 32)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: ENST00000616620.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

Genes affected

(HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370787	XR_932160.3	n.490-119T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000616620.1	n.29A>G		non_coding_transcript_exon_variant	1/1
SRP14-DT	ENST00000692845.1	n.802-1438A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39499 AN: 152058 Hom.: 5454 Cov.: 32

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.00942

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.253

GnomAD4 exome AF: 0.250 AC: 2 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 2 AN XY: 4

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.250

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.260 AC: 39526 AN: 152176 Hom.: 5464 Cov.: 32 AF XY: 0.254 AC XY: 18885 AN XY: 74410

Gnomad4 AFR AF: 0.290

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.00944

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.281

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.254

Alfa AF: 0.278 Hom.: 1262

Bravo AF: 0.250

Asia WGS AF: 0.120 AC: 417 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	0.80
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3923235; hg19: chr15-40371121;