1-109823461-T-C

Position:

• chr1-109823461-T-C

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 0.597 in 152,156 control chromosomes in the GnomAD database, including 29,900 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 0.60 (29900 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.171

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.109823461T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90796 AN: 152038 Hom.: 29850 Cov.: 32

Gnomad AFR AF: 0.856

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.597 AC: 90887 AN: 152156 Hom.: 29900 Cov.: 32 AF XY: 0.586 AC XY: 43612 AN XY: 74388

Gnomad4 AFR AF: 0.856

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.636

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.536

Gnomad4 FIN AF: 0.400

Gnomad4 NFE AF: 0.535

Gnomad4 OTH AF: 0.599

Alfa AF: 0.543 Hom.: 48331

Bravo AF: 0.609

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.2
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs484959; hg19: chr1-110366083;