rs2021840

Variant names:

• chr1-172674080-A-G
• rs2021840

Your query was ambiguous. Multiple possible variants found:

• chr1-172674080-A-G
• chr1-172674080-A-T

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 0.258 in 152,082 control chromosomes in the GnomAD database, including 5,425 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 0.26 (5425 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.461

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 (SAS) allele frequency at 95% confidence interval = 0.378 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: 0.258 AC: 39135 AN: 151964 Hom.: 5407 Cov.: 31

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.258 AC: 39196 AN: 152082 Hom.: 5425 Cov.: 31 AF XY: 0.255 AC XY: 18939 AN XY: 74336

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.412

Gnomad4 EAS AF: 0.0999

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.257

Gnomad4 OTH AF: 0.292

Alfa AF: 0.272 Hom.: 6696

Bravo AF: 0.263

Asia WGS AF: 0.266 AC: 926 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	3.1
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2021840; hg19: chr1-172643220;