1-106293321-T-C

Variant names:

• chr1-106293321-T-C
• rs1330225

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 0.376 in 151,776 control chromosomes in the GnomAD database, including 12,362 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 0.38 (12362 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.437

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.586 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: 0.376 AC: 57014 AN: 151660 Hom.: 12330 Cov.: 30

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.0133

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.376 AC: 57091 AN: 151776 Hom.: 12362 Cov.: 30 AF XY: 0.370 AC XY: 27445 AN XY: 74184

Gnomad4 AFR AF: 0.593

Gnomad4 AMR AF: 0.300

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.0136

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.382

Alfa AF: 0.331 Hom.: 3551

Bravo AF: 0.386

Asia WGS AF: 0.200 AC: 698 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	1.2
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1330225; hg19: chr1-106835943;