rs1330225

Positions:

• chr1-106293321-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;