1-177166627-A-G

Variant names:

• chr1-177166627-A-G
• rs6665358

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 0.156 in 152,174 control chromosomes in the GnomAD database, including 3,750 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 0.16 (3750 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.169
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.401 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: 0.156 AC: 23689 AN: 152056 Hom.: 3747 Cov.: 33

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0943

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.0742

Gnomad FIN AF: 0.0215

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0415

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.156 AC: 23712 AN: 152174 Hom.: 3750 Cov.: 33 AF XY: 0.154 AC XY: 11490 AN XY: 74420

African (AFR) AF: 0.406 AC: 16846 AN: 41470

American (AMR) AF: 0.105 AC: 1604 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0943 AC: 327 AN: 3468

East Asian (EAS) AF: 0.205 AC: 1061 AN: 5180

South Asian (SAS) AF: 0.0734 AC: 354 AN: 4820

European-Finnish (FIN) AF: 0.0215 AC: 228 AN: 10624

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.0414 AC: 2817 AN: 68000

Other (OTH) AF: 0.121 AC: 255 AN: 2112

Alfa AF: 0.118 Hom.: 348

Bravo AF: 0.175

Asia WGS AF: 0.156 AC: 540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.3
DANN	Benign	0.63
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs6665358; hg19: chr1-177135763;