rs883062

Variant names:

• chr1-42144196-G-A
• rs883062

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 0.428 in 152,138 control chromosomes in the GnomAD database, including 16,561 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 0.43 (16561 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.299

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.553 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: 0.428 AC: 65116 AN: 152020 Hom.: 16567 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.428 AC: 65118 AN: 152138 Hom.: 16561 Cov.: 32 AF XY: 0.428 AC XY: 31826 AN XY: 74386

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.497

Gnomad4 ASJ AF: 0.641

Gnomad4 EAS AF: 0.364

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.566

Gnomad4 NFE AF: 0.558

Gnomad4 OTH AF: 0.472

Alfa AF: 0.541 Hom.: 30077

Bravo AF: 0.413

Asia WGS AF: 0.339 AC: 1181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	7.7
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs883062; hg19: chr1-42609867;