1-109278889-T-G

Variant names:

• chr1-109278889-T-G
• rs602633

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 0.644 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.750

Gnomad4 ASJ AF: 0.829

Gnomad4 EAS AF: 0.935

Gnomad4 SAS AF: 0.750

Gnomad4 FIN AF: 0.776

Gnomad4 NFE AF: 0.781

Gnomad4 OTH AF: 0.704

Alfa AF: 0.775 Hom.: 42551

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs602633; hg19: chr1-109821511;