8-92487589-T-C

Position:

• chr8-92487589-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000648652.1(ENSG00000253634):​n.1052+12167A>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 0.523 in 152,052 control chromosomes in the GnomAD database, including 21,453 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 0.52 (21453 hom., cov: 32)
• Consequence: ENST00000648652.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.727

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.608 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375639	XR_007061005.1	n.425+13149A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000648652.1	n.1052+12167A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79511 AN: 151934 Hom.: 21439 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.523 AC: 79571 AN: 152052 Hom.: 21453 Cov.: 32 AF XY: 0.530 AC XY: 39379 AN XY: 74312

Gnomad4 AFR AF: 0.390

Gnomad4 AMR AF: 0.523

Gnomad4 ASJ AF: 0.591

Gnomad4 EAS AF: 0.484

Gnomad4 SAS AF: 0.626

Gnomad4 FIN AF: 0.637

Gnomad4 NFE AF: 0.577

Gnomad4 OTH AF: 0.531

Alfa AF: 0.567 Hom.: 50116

Bravo AF: 0.509

Asia WGS AF: 0.547 AC: 1899 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	17
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1597301; hg19: chr8-93499817;