rs2859228

Positions:

• chr1-172644101-A-G
• chr1-172644101-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 0.459 in 151,788 control chromosomes in the GnomAD database, including 16,238 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 0.46 (16238 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.585

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.566 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: 0.459 AC: 69652 AN: 151670 Hom.: 16214 Cov.: 30

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.459 AC: 69717 AN: 151788 Hom.: 16238 Cov.: 30 AF XY: 0.462 AC XY: 34273 AN XY: 74186

Gnomad4 AFR AF: 0.444

Gnomad4 AMR AF: 0.403

Gnomad4 ASJ AF: 0.478

Gnomad4 EAS AF: 0.312

Gnomad4 SAS AF: 0.584

Gnomad4 FIN AF: 0.509

Gnomad4 NFE AF: 0.474

Gnomad4 OTH AF: 0.458

Alfa AF: 0.467 Hom.: 34801

Bravo AF: 0.443

Asia WGS AF: 0.472 AC: 1640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.38
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2859228; hg19: chr1-172613241;