rs8038234

Variant names:

• chr15-23801570-T-G
• rs8038234
• ENST00000658937.2:n.510-23154T>G

Variant summary

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

The ENST00000658937.2(ENSG00000286973):​n.510-23154T>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 ENST00000658937.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93
• Publications: 2 publications found

Genes affected

ENSG00000286973 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000658937.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286973	ENST00000658937.2		n.510-23154T>G		intron	N/A
	ENSG00000286973	ENST00000844005.1		n.601-23154T>G		intron	N/A
	ENSG00000286973	ENST00000844006.1		n.472-23154T>G		intron	N/A

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

African (AFR) AF: 0.262 AC: 10888 AN: 41490

American (AMR) AF: 0.140 AC: 2141 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 415 AN: 3470

East Asian (EAS) AF: 0.0305 AC: 158 AN: 5180

South Asian (SAS) AF: 0.0563 AC: 272 AN: 4832

European-Finnish (FIN) AF: 0.110 AC: 1169 AN: 10602

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8752 AN: 68008

Other (OTH) AF: 0.168 AC: 356 AN: 2114

Alfa AF: 0.137 Hom.: 2852

Bravo AF: 0.170

Asia WGS AF: 0.0500 AC: 174 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.56
DANN	Benign	0.43
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs8038234; hg19: chr15-24046717;