rs1330226

Variant names:

• chr1-106300553-C-T
• rs1330226

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 0.671 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.846 AC: 35025 AN: 41400

American (AMR) AF: 0.553 AC: 8405 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.724 AC: 2511 AN: 3466

East Asian (EAS) AF: 0.172 AC: 881 AN: 5134

South Asian (SAS) AF: 0.550 AC: 2643 AN: 4806

European-Finnish (FIN) AF: 0.587 AC: 6087 AN: 10370

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.646 AC: 43782 AN: 67794

Other (OTH) AF: 0.676 AC: 1419 AN: 2100

Alfa AF: 0.647 Hom.: 16352

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
PhyloP100		0.084

Splicing

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

Other links and lift over

dbSNP: rs1330226; hg19: chr1-106843175;