chr1-151958169-T-C

Variant names:

• chr1-151958169-T-C
• rs6693388

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 0.316 in 152,176 control chromosomes in the GnomAD database, including 7,822 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 0.32 (7822 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.519 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: 0.316 AC: 48065 AN: 152058 Hom.: 7822 Cov.: 33

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.316 AC: 48095 AN: 152176 Hom.: 7822 Cov.: 33 AF XY: 0.317 AC XY: 23604 AN XY: 74400

African (AFR) AF: 0.317 AC: 13169 AN: 41492

American (AMR) AF: 0.250 AC: 3821 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1798 AN: 3468

East Asian (EAS) AF: 0.266 AC: 1377 AN: 5186

South Asian (SAS) AF: 0.537 AC: 2590 AN: 4826

European-Finnish (FIN) AF: 0.272 AC: 2872 AN: 10578

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21404 AN: 68004

Other (OTH) AF: 0.309 AC: 654 AN: 2116

Alfa AF: 0.323 Hom.: 2184

Bravo AF: 0.309

Asia WGS AF: 0.334 AC: 1161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.73
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs6693388; hg19: chr1-151930645;