1-84295665-T-C

Position:

• chr1-84295665-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 0.787 in 152,148 control chromosomes in the GnomAD database, including 47,684 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 0.79 (47684 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.84295665T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.787 AC: 119643 AN: 152030 Hom.: 47662 Cov.: 32

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.792

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.870

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.829

Gnomad OTH AF: 0.791

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

GnomAD4 genome AF: 0.787 AC: 119709 AN: 152148 Hom.: 47684 Cov.: 32 AF XY: 0.788 AC XY: 58648 AN XY: 74400

Gnomad4 AFR AF: 0.662

Gnomad4 AMR AF: 0.792

Gnomad4 ASJ AF: 0.882

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.871

Gnomad4 FIN AF: 0.814

Gnomad4 NFE AF: 0.829

Gnomad4 OTH AF: 0.791

Alfa AF: 0.839 Hom.: 18172

Bravo AF: 0.779

Asia WGS AF: 0.911 AC: 3165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1085093; hg19: chr1-84761348;