1-219602090-A-G

Variant names:

• chr1-219602090-A-G
• rs994767

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.604 AC: 24818 AN: 41058

American (AMR) AF: 0.463 AC: 7025 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.627 AC: 2168 AN: 3458

East Asian (EAS) AF: 0.651 AC: 3304 AN: 5074

South Asian (SAS) AF: 0.618 AC: 2942 AN: 4758

European-Finnish (FIN) AF: 0.540 AC: 5650 AN: 10470

Middle Eastern (MID) AF: 0.596 AC: 174 AN: 292

European-Non Finnish (NFE) AF: 0.535 AC: 36214 AN: 67748

Other (OTH) AF: 0.567 AC: 1188 AN: 2094

Alfa AF: 0.501 Hom.: 4521

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
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs994767; hg19: chr1-219775432;