rs2807845

Positions:

• chr1-220822945-G-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 0.472 in 151,998 control chromosomes in the GnomAD database, including 16,976 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 0.47 (16976 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.514 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: 0.471 AC: 71602 AN: 151880 Hom.: 16945 Cov.: 32

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.472 AC: 71679 AN: 151998 Hom.: 16976 Cov.: 32 AF XY: 0.471 AC XY: 35029 AN XY: 74296

Gnomad4 AFR AF: 0.520

Gnomad4 AMR AF: 0.456

Gnomad4 ASJ AF: 0.413

Gnomad4 EAS AF: 0.481

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.472

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.455

Alfa AF: 0.467 Hom.: 2372

Bravo AF: 0.475

Asia WGS AF: 0.454 AC: 1581 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	0.026
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2807845; hg19: chr1-220996287;