1-150877559-A-G

Variant names:

• chr1-150877559-A-G
• rs7517566

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 0.891 in 152,210 control chromosomes in the GnomAD database, including 60,442 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 0.89 (60442 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.902 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: 0.891 AC: 135486 AN: 152092 Hom.: 60419 Cov.: 32

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.869

Gnomad AMR AF: 0.915

Gnomad ASJ AF: 0.851

Gnomad EAS AF: 0.810

Gnomad SAS AF: 0.873

Gnomad FIN AF: 0.904

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.905

Gnomad OTH AF: 0.898

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

GnomAD4 genome AF: 0.891 AC: 135564 AN: 152210 Hom.: 60442 Cov.: 32 AF XY: 0.891 AC XY: 66285 AN XY: 74424

Gnomad4 AFR AF: 0.870

Gnomad4 AMR AF: 0.915

Gnomad4 ASJ AF: 0.851

Gnomad4 EAS AF: 0.810

Gnomad4 SAS AF: 0.874

Gnomad4 FIN AF: 0.904

Gnomad4 NFE AF: 0.905

Gnomad4 OTH AF: 0.897

Alfa AF: 0.900 Hom.: 60953

Bravo AF: 0.889

Asia WGS AF: 0.835 AC: 2907 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.7
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7517566; hg19: chr1-150850035;