8-137869317-C-T

Position:

• chr8-137869317-C-T

Variant summary

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

The ENST00000518973.1(ENSG00000253288):​n.515-31432G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.881 in 152,146 control chromosomes in the GnomAD database, including 59,498 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 0.88 (59498 hom., cov: 30)
• Consequence: ENSG00000253288 ENST00000518973.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88

Genes affected

ENSG00000253288 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.928 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC401478	NR_161374.1	n.574-31432G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000253288	ENST00000518973.1	n.515-31432G>A		intron_variant		2
ENSG00000254361	ENST00000519652.2	n.230+12198C>T		intron_variant		4
ENSG00000253288	ENST00000657186.1	n.602-31432G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.881 AC: 133870 AN: 152030 Hom.: 59442 Cov.: 30

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.915

Gnomad ASJ AF: 0.899

Gnomad EAS AF: 0.950

Gnomad SAS AF: 0.924

Gnomad FIN AF: 0.936

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.931

Gnomad OTH AF: 0.880

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

GnomAD4 genome AF: 0.881 AC: 133981 AN: 152146 Hom.: 59498 Cov.: 30 AF XY: 0.883 AC XY: 65645 AN XY: 74372

Gnomad4 AFR AF: 0.755

Gnomad4 AMR AF: 0.915

Gnomad4 ASJ AF: 0.899

Gnomad4 EAS AF: 0.950

Gnomad4 SAS AF: 0.924

Gnomad4 FIN AF: 0.936

Gnomad4 NFE AF: 0.931

Gnomad4 OTH AF: 0.881

Alfa AF: 0.889 Hom.: 10633

Bravo AF: 0.873

Asia WGS AF: 0.916 AC: 3185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.45
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1511849; hg19: chr8-138881560;