1-153356595-T-C

Variant names:

• chr1-153356595-T-C
• rs3014866

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 0.587 in 152,028 control chromosomes in the GnomAD database, including 26,673 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 0.59 (26673 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.511
• Publications: 19 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 (AFR) allele frequency at 95% confidence interval = 0.693 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: 0.587 AC: 89144 AN: 151908 Hom.: 26637 Cov.: 32

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.587 AC: 89237 AN: 152028 Hom.: 26673 Cov.: 32 AF XY: 0.588 AC XY: 43681 AN XY: 74304

African (AFR) AF: 0.700 AC: 29014 AN: 41462

American (AMR) AF: 0.565 AC: 8632 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1975 AN: 3468

East Asian (EAS) AF: 0.617 AC: 3191 AN: 5170

South Asian (SAS) AF: 0.397 AC: 1909 AN: 4814

European-Finnish (FIN) AF: 0.623 AC: 6580 AN: 10562

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.533 AC: 36192 AN: 67954

Other (OTH) AF: 0.578 AC: 1220 AN: 2110

Alfa AF: 0.549 Hom.: 42466

Bravo AF: 0.592

Asia WGS AF: 0.530 AC: 1844 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	0.94
DANN	Benign	0.44
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs3014866; hg19: chr1-153329071; COSMIC: COSV64199899;