chr1-152618187-T-C

Variant names:

• chr1-152618187-T-C
• rs6693105

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 0.589 in 152,028 control chromosomes in the GnomAD database, including 26,922 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 (26922 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.590 AC: 89570 AN: 151912 Hom.: 26912 Cov.: 32

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.589 AC: 89615 AN: 152028 Hom.: 26922 Cov.: 32 AF XY: 0.594 AC XY: 44144 AN XY: 74310

African (AFR) AF: 0.457 AC: 18949 AN: 41474

American (AMR) AF: 0.625 AC: 9551 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.622 AC: 2161 AN: 3472

East Asian (EAS) AF: 0.613 AC: 3165 AN: 5160

South Asian (SAS) AF: 0.631 AC: 3038 AN: 4814

European-Finnish (FIN) AF: 0.662 AC: 6994 AN: 10558

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.645 AC: 43816 AN: 67966

Other (OTH) AF: 0.588 AC: 1238 AN: 2104

Alfa AF: 0.611 Hom.: 6237

Bravo AF: 0.578

Asia WGS AF: 0.584 AC: 2033 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.9
DANN	Benign	0.72
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs6693105; hg19: chr1-152590663;