rs2208921

Positions:

• chr1-189711247-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 0.453 in 151,986 control chromosomes in the GnomAD database, including 15,941 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 0.45 (15941 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.491 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: 0.453 AC: 68777 AN: 151868 Hom.: 15932 Cov.: 33

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.453 AC: 68816 AN: 151986 Hom.: 15941 Cov.: 33 AF XY: 0.451 AC XY: 33464 AN XY: 74258

Gnomad4 AFR AF: 0.395

Gnomad4 AMR AF: 0.371

Gnomad4 ASJ AF: 0.476

Gnomad4 EAS AF: 0.455

Gnomad4 SAS AF: 0.410

Gnomad4 FIN AF: 0.529

Gnomad4 NFE AF: 0.495

Gnomad4 OTH AF: 0.439

Alfa AF: 0.452 Hom.: 2487

Bravo AF: 0.440

Asia WGS AF: 0.419 AC: 1461 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.4
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2208921; hg19: chr1-189680377; COSMIC: COSV60003442;