8-81507193-G-C

Position:

• chr8-81507193-G-C

Variant summary

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

The ENST00000524085.2(ENSG00000253859):​n.434+9141G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 151,986 control chromosomes in the GnomAD database, including 12,744 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 0.38 (12744 hom., cov: 32)
• Consequence: ENSG00000253859 ENST00000524085.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660

Genes affected

ENSG00000253859 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101927118	XR_001745980.2	n.518-18650G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000253859	ENST00000524085.2	n.434+9141G>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58362 AN: 151868 Hom.: 12698 Cov.: 32

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.385 AC: 58470 AN: 151986 Hom.: 12744 Cov.: 32 AF XY: 0.382 AC XY: 28395 AN XY: 74312

Gnomad4 AFR AF: 0.593

Gnomad4 AMR AF: 0.403

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.380

Alfa AF: 0.340 Hom.: 1169

Bravo AF: 0.401

Asia WGS AF: 0.296 AC: 1029 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	2.1
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1843560; hg19: chr8-82419428;