rs8038234

Variant names:

• chr15-23801570-T-G
• rs8038234
• ENST00000658937.1:n.460-23154T>G

Variant summary

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

The ENST00000658937.1(ENSG00000286973):​n.460-23154T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,194 control chromosomes in the GnomAD database, including 2,260 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 0.16 (2260 hom., cov: 33)
• Consequence: ENSG00000286973 ENST00000658937.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93

Genes affected

ENSG00000286973 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.258 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
ENSG00000286973	ENST00000658937.1	n.460-23154T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24291 AN: 152076 Hom.: 2250 Cov.: 33

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.0302

Gnomad SAS AF: 0.0575

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.160 AC: 24320 AN: 152194 Hom.: 2260 Cov.: 33 AF XY: 0.155 AC XY: 11504 AN XY: 74406

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.0305

Gnomad4 SAS AF: 0.0563

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.168

Alfa AF: 0.132 Hom.: 1925

Bravo AF: 0.170

Asia WGS AF: 0.0500 AC: 174 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.56
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8038234; hg19: chr15-24046717;