1-9280979-C-T

Variant names:

• chr1-9280979-C-T
• rs916380

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 0.543 in 151,944 control chromosomes in the GnomAD database, including 22,876 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 0.54 (22876 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.114
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.669 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: 0.543 AC: 82431 AN: 151826 Hom.: 22871 Cov.: 31

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.543 AC: 82456 AN: 151944 Hom.: 22876 Cov.: 31 AF XY: 0.544 AC XY: 40416 AN XY: 74298

African (AFR) AF: 0.426 AC: 17658 AN: 41432

American (AMR) AF: 0.560 AC: 8555 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1889 AN: 3470

East Asian (EAS) AF: 0.688 AC: 3543 AN: 5150

South Asian (SAS) AF: 0.629 AC: 3029 AN: 4816

European-Finnish (FIN) AF: 0.577 AC: 6091 AN: 10562

Middle Eastern (MID) AF: 0.473 AC: 138 AN: 292

European-Non Finnish (NFE) AF: 0.587 AC: 39842 AN: 67928

Other (OTH) AF: 0.550 AC: 1156 AN: 2100

Alfa AF: 0.575 Hom.: 96895

Bravo AF: 0.537

Asia WGS AF: 0.665 AC: 2312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.0
DANN	Benign	0.70
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs916380; hg19: chr1-9341038; COSMIC: COSV72764856;