3-110808404-G-T

Position:

• chr3-110808404-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 0.57 in 150,622 control chromosomes in the GnomAD database, including 29,961 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 0.57 (29961 hom., cov: 29)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.886

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) 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
		n.110808404G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.571 AC: 85940 AN: 150502 Hom.: 29969 Cov.: 29

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.780

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.570 AC: 85925 AN: 150622 Hom.: 29961 Cov.: 29 AF XY: 0.567 AC XY: 41681 AN XY: 73450

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.634

Gnomad4 ASJ AF: 0.693

Gnomad4 EAS AF: 0.393

Gnomad4 SAS AF: 0.686

Gnomad4 FIN AF: 0.683

Gnomad4 NFE AF: 0.783

Gnomad4 OTH AF: 0.623

Alfa AF: 0.588 Hom.: 6044

Bravo AF: 0.546

Asia WGS AF: 0.527 AC: 1822 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.25
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: rs1462309; hg19: chr3-110527251;