1-105414627-T-G

Position:

• chr1-105414627-T-G

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 0.434 in 151,842 control chromosomes in the GnomAD database, including 14,695 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 0.43 (14695 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.461 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: 0.434 AC: 65854 AN: 151724 Hom.: 14690 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.434 AC: 65882 AN: 151842 Hom.: 14695 Cov.: 32 AF XY: 0.432 AC XY: 32065 AN XY: 74192

Gnomad4 AFR AF: 0.388

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.517

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.305

Gnomad4 FIN AF: 0.516

Gnomad4 NFE AF: 0.466

Gnomad4 OTH AF: 0.418

Alfa AF: 0.451 Hom.: 11766

Bravo AF: 0.427

Asia WGS AF: 0.263 AC: 915 AN: 3470

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	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs987243; hg19: chr1-105957249;