chr1-106300553-C-T

Position:

• chr1-106300553-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;