rs2021840

chr1-172674080-A-Gchr1-172674080-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;