1-177166627-A-G

Variant names:

• chr1-177166627-A-G
• rs6665358

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.406

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.0943

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.0734

Gnomad4 FIN AF: 0.0215

Gnomad4 NFE AF: 0.0414

Gnomad4 OTH AF: 0.121

Alfa AF: 0.106 Hom.: 275

Bravo AF: 0.175

Asia WGS AF: 0.156 AC: 540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6665358; hg19: chr1-177135763;