1-17287242-A-T

Variant names:

• chr1-17287242-A-T
• rs2977305

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 0.841 in 152,234 control chromosomes in the GnomAD database, including 54,027 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 0.84 (54027 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.871
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.841 AC: 127972 AN: 152116 Hom.: 53991 Cov.: 33

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.885

Gnomad ASJ AF: 0.867

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.948

Gnomad FIN AF: 0.813

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.841

Gnomad OTH AF: 0.855

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

GnomAD4 genome AF: 0.841 AC: 128062 AN: 152234 Hom.: 54027 Cov.: 33 AF XY: 0.842 AC XY: 62675 AN XY: 74430

African (AFR) AF: 0.802 AC: 33306 AN: 41546

American (AMR) AF: 0.885 AC: 13534 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.867 AC: 3011 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5176 AN: 5180

South Asian (SAS) AF: 0.948 AC: 4580 AN: 4830

European-Finnish (FIN) AF: 0.813 AC: 8609 AN: 10586

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.841 AC: 57166 AN: 68008

Other (OTH) AF: 0.856 AC: 1808 AN: 2112

Alfa AF: 0.832 Hom.: 6171

Bravo AF: 0.845

Asia WGS AF: 0.958 AC: 3331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.3
DANN	Benign	0.55
PhyloP100		0.87

Splicing

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

Other links and lift over

dbSNP: rs2977305; hg19: chr1-17613737;