rs883062

Positions:

• chr1-42144196-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;