8-109051931-G-T

Position:

• chr8-109051931-G-T

Variant summary

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

The variant allele was found at a frequency of 0.637 in 152,080 control chromosomes in the GnomAD database, including 31,744 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 0.64 (31744 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.329

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.109051931G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000253796	ENST00000522244.1	n.130-7804C>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96858 AN: 151962 Hom.: 31708 Cov.: 32

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.637 AC: 96949 AN: 152080 Hom.: 31744 Cov.: 32 AF XY: 0.639 AC XY: 47473 AN XY: 74326

Gnomad4 AFR AF: 0.769

Gnomad4 AMR AF: 0.718

Gnomad4 ASJ AF: 0.519

Gnomad4 EAS AF: 0.715

Gnomad4 SAS AF: 0.605

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.558

Gnomad4 OTH AF: 0.618

Alfa AF: 0.550 Hom.: 3228

Bravo AF: 0.660

Asia WGS AF: 0.675 AC: 2346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4276659; hg19: chr8-110064160;