1-109278889-T-G

Variant names:

• chr1-109278889-T-G
• rs602633

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 0.644 in 152,118 control chromosomes in the GnomAD database, including 35,696 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 0.64 (35696 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.381
• Publications: 131 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.913 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: 0.645 AC: 97975 AN: 152002 Hom.: 35694 Cov.: 32

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.658

Gnomad AMR AF: 0.750

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.934

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.776

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.701

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

GnomAD4 genome AF: 0.644 AC: 97996 AN: 152118 Hom.: 35696 Cov.: 32 AF XY: 0.648 AC XY: 48188 AN XY: 74388

African (AFR) AF: 0.279 AC: 11562 AN: 41484

American (AMR) AF: 0.750 AC: 11467 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.829 AC: 2875 AN: 3470

East Asian (EAS) AF: 0.935 AC: 4823 AN: 5160

South Asian (SAS) AF: 0.750 AC: 3617 AN: 4824

European-Finnish (FIN) AF: 0.776 AC: 8228 AN: 10598

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.781 AC: 53085 AN: 67980

Other (OTH) AF: 0.704 AC: 1488 AN: 2114

Alfa AF: 0.742 Hom.: 125010

Bravo AF: 0.626

Asia WGS AF: 0.812 AC: 2823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	12
DANN	Benign	0.79
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs602633; hg19: chr1-109821511;