chr1-8127151-A-G

Position:

• chr1-8127151-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 0.219 in 151,752 control chromosomes in the GnomAD database, including 5,504 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 0.22 (5504 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.676 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: 0.219 AC: 33177 AN: 151638 Hom.: 5486 Cov.: 33

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.0824

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.219 AC: 33240 AN: 151752 Hom.: 5504 Cov.: 33 AF XY: 0.225 AC XY: 16673 AN XY: 74214

Gnomad4 AFR AF: 0.308

Gnomad4 AMR AF: 0.358

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.695

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.0824

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.216

Alfa AF: 0.146 Hom.: 4944

Bravo AF: 0.246

Asia WGS AF: 0.448 AC: 1555 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.84
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4908736; hg19: chr1-8187211;