rs8038068

Variant names:

• chr15-43622175-T-C
• rs8038068
• ENST00000643290.1:n.86-3099A>G

Variant summary

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

The ENST00000643290.1(ENSG00000284772):​n.86-3099A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 151,548 control chromosomes in the GnomAD database, including 1,788 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 0.14 (1788 hom., cov: 31)
• Consequence: ENSG00000284772 ENST00000643290.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.434

Genes affected

ENSG00000284772 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.173 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
ENSG00000284772	ENST00000643290.1	n.86-3099A>G		intron_variant	Intron 1 of 8			ENSP00000495476.1

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20595 AN: 151422 Hom.: 1787 Cov.: 31

Gnomad AFR AF: 0.0867

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.136 AC: 20610 AN: 151548 Hom.: 1788 Cov.: 31 AF XY: 0.133 AC XY: 9838 AN XY: 73984

Gnomad4 AFR AF: 0.0872

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.00136

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.152

Alfa AF: 0.149 Hom.: 246

Bravo AF: 0.134

Asia WGS AF: 0.0740 AC: 261 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	2.5
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8038068; hg19: chr15-43914373;