rs7181230

Variant names:

• chr15-40068540-A-G
• rs7181230
• ENST00000655221.1:n.295-5213A>G

Variant summary

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

The ENST00000655221.1(SRP14-DT):​n.295-5213A>G variant causes a intron 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 ENST00000655221.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.758
• Publications: 32 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=-0.84).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SRP14-DT	ENST00000655221.1	n.295-5213A>G		intron_variant	Intron 2 of 3
SRP14-DT	ENST00000692845.1	n.295-5213A>G		intron_variant	Intron 2 of 4
SRP14-DT	ENST00000746676.1	n.292-19159A>G		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.304 AC: 12524 AN: 41166

American (AMR) AF: 0.222 AC: 3377 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1257 AN: 3442

East Asian (EAS) AF: 0.189 AC: 963 AN: 5102

South Asian (SAS) AF: 0.310 AC: 1474 AN: 4750

European-Finnish (FIN) AF: 0.359 AC: 3638 AN: 10136

Middle Eastern (MID) AF: 0.361 AC: 104 AN: 288

European-Non Finnish (NFE) AF: 0.337 AC: 22767 AN: 67618

Other (OTH) AF: 0.305 AC: 640 AN: 2100

Alfa AF: 0.327 Hom.: 35590

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
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs7181230; hg19: chr15-40360741;