1-164529929-A-G

Position:

• chr1-164529929-A-G

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 0.213 in 152,048 control chromosomes in the GnomAD database, including 4,792 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 0.21 (4792 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32360 AN: 151930 Hom.: 4782 Cov.: 32

Gnomad AFR AF: 0.0461

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.213 AC: 32381 AN: 152048 Hom.: 4792 Cov.: 32 AF XY: 0.221 AC XY: 16395 AN XY: 74314

Gnomad4 AFR AF: 0.0460

Gnomad4 AMR AF: 0.353

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.637

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.217

Alfa AF: 0.221 Hom.: 525

Bravo AF: 0.218

Asia WGS AF: 0.450 AC: 1561 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.7
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10918027; hg19: chr1-164499166;