1-84295665-T-C

Variant names:

• chr1-84295665-T-C
• rs1085093

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;