1-80481158-T-C

Variant names:

• chr1-80481158-T-C
• rs11163027

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.265 AC: 10960 AN: 41410

American (AMR) AF: 0.144 AC: 2189 AN: 15172

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 607 AN: 3466

East Asian (EAS) AF: 0.168 AC: 869 AN: 5168

South Asian (SAS) AF: 0.195 AC: 940 AN: 4822

European-Finnish (FIN) AF: 0.104 AC: 1098 AN: 10570

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9630 AN: 67834

Other (OTH) AF: 0.171 AC: 360 AN: 2104

Alfa AF: 0.158 Hom.: 1901

Bravo AF: 0.183

Asia WGS AF: 0.155 AC: 538 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.52
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs11163027; hg19: chr1-80946843;