1-161743067-C-T

Variant names:

• chr1-161743067-C-T
• rs1027702

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 0.51 in 151,926 control chromosomes in the GnomAD database, including 22,859 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 0.51 (22859 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.146
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.809 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: 0.510 AC: 77369 AN: 151806 Hom.: 22817 Cov.: 31

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.510 AC: 77458 AN: 151926 Hom.: 22859 Cov.: 31 AF XY: 0.506 AC XY: 37557 AN XY: 74246

African (AFR) AF: 0.816 AC: 33845 AN: 41458

American (AMR) AF: 0.374 AC: 5710 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1242 AN: 3468

East Asian (EAS) AF: 0.699 AC: 3623 AN: 5184

South Asian (SAS) AF: 0.388 AC: 1865 AN: 4810

European-Finnish (FIN) AF: 0.368 AC: 3875 AN: 10536

Middle Eastern (MID) AF: 0.432 AC: 126 AN: 292

European-Non Finnish (NFE) AF: 0.381 AC: 25871 AN: 67912

Other (OTH) AF: 0.470 AC: 993 AN: 2112

Alfa AF: 0.417 Hom.: 59642

Bravo AF: 0.522

Asia WGS AF: 0.519 AC: 1803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.6
DANN	Benign	0.79
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs1027702; hg19: chr1-161712857;