rs1330226

Variant names:

• chr1-106300553-C-T
• rs1330226

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 0.671 in 151,484 control chromosomes in the GnomAD database, including 35,736 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 0.67 (35736 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0840

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.839 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: 0.671 AC: 101578 AN: 151368 Hom.: 35705 Cov.: 30

Gnomad AFR AF: 0.846

Gnomad AMI AF: 0.747

Gnomad AMR AF: 0.554

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.550

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.671 AC: 101654 AN: 151484 Hom.: 35736 Cov.: 30 AF XY: 0.661 AC XY: 48908 AN XY: 74008

Gnomad4 AFR AF: 0.846

Gnomad4 AMR AF: 0.553

Gnomad4 ASJ AF: 0.724

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.550

Gnomad4 FIN AF: 0.587

Gnomad4 NFE AF: 0.646

Gnomad4 OTH AF: 0.676

Alfa AF: 0.647 Hom.: 14714

Bravo AF: 0.673

Asia WGS AF: 0.404 AC: 1398 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.0
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1330226; hg19: chr1-106843175;