1-80268896-C-T

Position:

• chr1-80268896-C-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 0.593 in 151,870 control chromosomes in the GnomAD database, including 27,262 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 0.59 (27262 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.243

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 (AMR) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.593 AC: 90000 AN: 151752 Hom.: 27248 Cov.: 31

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.635

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.593 AC: 90049 AN: 151870 Hom.: 27262 Cov.: 31 AF XY: 0.593 AC XY: 43984 AN XY: 74220

Gnomad4 AFR AF: 0.497

Gnomad4 AMR AF: 0.673

Gnomad4 ASJ AF: 0.635

Gnomad4 EAS AF: 0.458

Gnomad4 SAS AF: 0.446

Gnomad4 FIN AF: 0.683

Gnomad4 NFE AF: 0.640

Gnomad4 OTH AF: 0.584

Alfa AF: 0.618 Hom.: 16347

Bravo AF: 0.590

Asia WGS AF: 0.434 AC: 1511 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	1.2
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: rs11162963; hg19: chr1-80734581;