1-152467700-A-T

Variant names:

• chr1-152467700-A-T
• rs11205006

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.673

Gnomad4 AMR AF: 0.767

Gnomad4 ASJ AF: 0.806

Gnomad4 EAS AF: 0.782

Gnomad4 SAS AF: 0.743

Gnomad4 FIN AF: 0.785

Gnomad4 NFE AF: 0.727

Gnomad4 OTH AF: 0.746

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11205006; hg19: chr1-152440176;