chr1-157701026-A-G

Position:

• chr1-157701026-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 0.557 in 151,998 control chromosomes in the GnomAD database, including 26,487 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 0.56 (26487 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.387

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84592 AN: 151880 Hom.: 26432 Cov.: 31

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.557 AC: 84696 AN: 151998 Hom.: 26487 Cov.: 31 AF XY: 0.549 AC XY: 40803 AN XY: 74276

Gnomad4 AFR AF: 0.868

Gnomad4 AMR AF: 0.485

Gnomad4 ASJ AF: 0.465

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.419

Gnomad4 NFE AF: 0.441

Gnomad4 OTH AF: 0.532

Alfa AF: 0.460 Hom.: 30820

Bravo AF: 0.580

Asia WGS AF: 0.435 AC: 1513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
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: rs7528684; hg19: chr1-157670816;