rs8038234

Positions:

• chr15-23801570-T-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, non coding transcript 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: ENST00000658937.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000658937.1	n.460-23154T>G		intron_variant, non_coding_transcript_variant

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;