1-80481158-T-C

Position:

• chr1-80481158-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 0.177 in 151,750 control chromosomes in the GnomAD database, including 2,711 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 0.18 (2711 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.654

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 (AFR) allele frequency at 95% confidence interval = 0.261 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: 0.177 AC: 26830 AN: 151630 Hom.: 2703 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.177 AC: 26854 AN: 151750 Hom.: 2711 Cov.: 32 AF XY: 0.174 AC XY: 12920 AN XY: 74170

Gnomad4 AFR AF: 0.265

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.171

Alfa AF: 0.158 Hom.: 1129

Bravo AF: 0.183

Asia WGS AF: 0.155 AC: 538 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11163027; hg19: chr1-80946843;