1-152467700-A-T

Variant names:

• chr1-152467700-A-T
• rs11205006

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 0.726 in 151,616 control chromosomes in the GnomAD database, including 39,987 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 0.73 (39987 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.762 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: 0.726 AC: 109980 AN: 151498 Hom.: 39957 Cov.: 32

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.806

Gnomad EAS AF: 0.782

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.785

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.727

Gnomad OTH AF: 0.743

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

GnomAD4 genome AF: 0.726 AC: 110058 AN: 151616 Hom.: 39987 Cov.: 32 AF XY: 0.731 AC XY: 54143 AN XY: 74100

African (AFR) AF: 0.673 AC: 27812 AN: 41300

American (AMR) AF: 0.767 AC: 11686 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.806 AC: 2794 AN: 3468

East Asian (EAS) AF: 0.782 AC: 4024 AN: 5144

South Asian (SAS) AF: 0.743 AC: 3578 AN: 4816

European-Finnish (FIN) AF: 0.785 AC: 8237 AN: 10498

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.727 AC: 49339 AN: 67854

Other (OTH) AF: 0.746 AC: 1568 AN: 2102

Alfa AF: 0.721 Hom.: 4838

Bravo AF: 0.722

Asia WGS AF: 0.766 AC: 2662 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.54
PhyloP100		0.042

Splicing

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

Other links and lift over

dbSNP: rs11205006; hg19: chr1-152440176;