chr1-80744440-G-A

Variant names:

• chr1-80744440-G-A
• rs2105126

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 0.0965 in 152,002 control chromosomes in the GnomAD database, including 967 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 0.096 (967 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.292
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0966 AC: 14667 AN: 151886 Hom.: 967 Cov.: 32

Gnomad AFR AF: 0.0258

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.0780

Gnomad ASJ AF: 0.0876

Gnomad EAS AF: 0.000583

Gnomad SAS AF: 0.0463

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.0833

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.0865

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

GnomAD4 genome AF: 0.0965 AC: 14665 AN: 152002 Hom.: 967 Cov.: 32 AF XY: 0.0960 AC XY: 7134 AN XY: 74286

African (AFR) AF: 0.0257 AC: 1066 AN: 41492

American (AMR) AF: 0.0779 AC: 1189 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0876 AC: 304 AN: 3470

East Asian (EAS) AF: 0.000584 AC: 3 AN: 5136

South Asian (SAS) AF: 0.0464 AC: 223 AN: 4808

European-Finnish (FIN) AF: 0.159 AC: 1674 AN: 10544

Middle Eastern (MID) AF: 0.0828 AC: 24 AN: 290

European-Non Finnish (NFE) AF: 0.146 AC: 9908 AN: 67980

Other (OTH) AF: 0.0856 AC: 180 AN: 2102

Alfa AF: 0.127 Hom.: 689

Bravo AF: 0.0880

Asia WGS AF: 0.0310 AC: 108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.25
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs2105126; hg19: chr1-81210125;