chr1-219602090-A-G

Position:

• chr1-219602090-A-G

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 0.556 in 151,030 control chromosomes in the GnomAD database, including 23,642 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 0.56 (23642 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.633 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: 0.557 AC: 84001 AN: 150922 Hom.: 23638 Cov.: 28

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.652

Gnomad SAS AF: 0.618

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.605

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.556 AC: 84041 AN: 151030 Hom.: 23642 Cov.: 28 AF XY: 0.556 AC XY: 41044 AN XY: 73754

Gnomad4 AFR AF: 0.604

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.627

Gnomad4 EAS AF: 0.651

Gnomad4 SAS AF: 0.618

Gnomad4 FIN AF: 0.540

Gnomad4 NFE AF: 0.535

Gnomad4 OTH AF: 0.567

Alfa AF: 0.424 Hom.: 1160

Bravo AF: 0.550

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.9
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: rs994767; hg19: chr1-219775432;