1-79780263-T-C

Variant names:

• chr1-79780263-T-C
• rs11162822

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 0.264 in 151,850 control chromosomes in the GnomAD database, including 5,732 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 0.26 (5732 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.405
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40010 AN: 151734 Hom.: 5717 Cov.: 31

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.264 AC: 40050 AN: 151850 Hom.: 5732 Cov.: 31 AF XY: 0.263 AC XY: 19512 AN XY: 74226

African (AFR) AF: 0.234 AC: 9698 AN: 41422

American (AMR) AF: 0.256 AC: 3904 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 913 AN: 3466

East Asian (EAS) AF: 0.609 AC: 3132 AN: 5146

South Asian (SAS) AF: 0.348 AC: 1671 AN: 4808

European-Finnish (FIN) AF: 0.186 AC: 1952 AN: 10494

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.261 AC: 17742 AN: 67942

Other (OTH) AF: 0.273 AC: 575 AN: 2104

Alfa AF: 0.256 Hom.: 1327

Bravo AF: 0.270

Asia WGS AF: 0.449 AC: 1555 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.74
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs11162822; hg19: chr1-80245948;