1-162990046-A-G

Variant names:

• chr1-162990046-A-G
• rs2841979

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 0.706 in 152,086 control chromosomes in the GnomAD database, including 38,146 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 0.71 (38146 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.335

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.79 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: 0.706 AC: 107220 AN: 151966 Hom.: 38113 Cov.: 32

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.790

Gnomad SAS AF: 0.811

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.699

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

GnomAD4 genome AF: 0.706 AC: 107309 AN: 152086 Hom.: 38146 Cov.: 32 AF XY: 0.705 AC XY: 52443 AN XY: 74346

Gnomad4 AFR AF: 0.762

Gnomad4 AMR AF: 0.708

Gnomad4 ASJ AF: 0.669

Gnomad4 EAS AF: 0.790

Gnomad4 SAS AF: 0.811

Gnomad4 FIN AF: 0.593

Gnomad4 NFE AF: 0.676

Gnomad4 OTH AF: 0.700

Alfa AF: 0.684 Hom.: 73112

Bravo AF: 0.716

Asia WGS AF: 0.803 AC: 2789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.9
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2841979; hg19: chr1-162959836;