8-22680913-C-T

Position:

• chr8-22680913-C-T

Variant summary

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

The ENST00000566457.1(ENSG00000261026):​n.3097G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.695 in 151,978 control chromosomes in the GnomAD database, including 36,928 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 0.70 (36923 hom., cov: 33)
  • Exomes 𝑓: 0.63 (5 hom.)
• Consequence: ENST00000566457.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.657

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.777 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986924	XR_001745827.2	n.5523C>T		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000566457.1	n.3097G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.695 AC: 105568 AN: 151828 Hom.: 36881 Cov.: 33

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.606

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.701

GnomAD4 exome AF: 0.625 AC: 20 AN: 32 Hom.: 5 Cov.: 0 AF XY: 0.708 AC XY: 17 AN XY: 24

Gnomad4 AFR exome AF: 1.00

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.611

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.695 AC: 105658 AN: 151946 Hom.: 36923 Cov.: 33 AF XY: 0.699 AC XY: 51954 AN XY: 74282

Gnomad4 AFR AF: 0.727

Gnomad4 AMR AF: 0.708

Gnomad4 ASJ AF: 0.671

Gnomad4 EAS AF: 0.797

Gnomad4 SAS AF: 0.623

Gnomad4 FIN AF: 0.742

Gnomad4 NFE AF: 0.665

Gnomad4 OTH AF: 0.700

Alfa AF: 0.679 Hom.: 17702

Bravo AF: 0.698

Asia WGS AF: 0.688 AC: 2392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	13
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10095121; hg19: chr8-22538426;