1-106793679-G-T

Position:

• chr1-106793679-G-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 0.185 in 152,094 control chromosomes in the GnomAD database, including 3,025 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 0.18 (3025 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.28 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: 0.184 AC: 28037 AN: 151976 Hom.: 3020 Cov.: 32

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.0784

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.185 AC: 28074 AN: 152094 Hom.: 3025 Cov.: 32 AF XY: 0.184 AC XY: 13712 AN XY: 74358

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.0784

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.163

Alfa AF: 0.133 Hom.: 1502

Bravo AF: 0.193

Asia WGS AF: 0.246 AC: 856 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.79
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12097821; hg19: chr1-107336301;