rs3923235

Variant names:

• chr15-40078920-A-G
• rs3923235
• ENST00000616620.1:n.29A>G

Variant summary

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

The ENST00000616620.1(SRP14-DT):​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: SRP14-DT ENST00000616620.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 7 publications found

Genes affected

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

ENSG00000259584 (HGNC:):

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000616620.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105370787	NR_188231.1		n.269-119T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SRP14-DT	ENST00000616620.1	TSL:6	n.29A>G		non_coding_transcript_exon	Exon 1 of 1
	SRP14-DT	ENST00000746677.1		n.832A>G		non_coding_transcript_exon	Exon 5 of 5
	SRP14-DT	ENST00000746678.1		n.709A>G		non_coding_transcript_exon	Exon 5 of 5

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.250 AC: 1 AN: 4

Other (OTH) AF: 0.500 AC: 1 AN: 2

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

African (AFR) AF: 0.290 AC: 12049 AN: 41488

American (AMR) AF: 0.167 AC: 2559 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 982 AN: 3472

East Asian (EAS) AF: 0.00944 AC: 49 AN: 5192

South Asian (SAS) AF: 0.208 AC: 1005 AN: 4832

European-Finnish (FIN) AF: 0.281 AC: 2972 AN: 10582

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 19020 AN: 67996

Other (OTH) AF: 0.254 AC: 536 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.80
DANN	Benign	0.31
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs3923235; hg19: chr15-40371121;