chr1-106756963-G-A

Position:

• chr1-106756963-G-A

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 0.164 in 151,850 control chromosomes in the GnomAD database, including 2,261 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 0.16 (2261 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.106756963G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24807 AN: 151732 Hom.: 2254 Cov.: 31

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.0762

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.164 AC: 24836 AN: 151850 Hom.: 2261 Cov.: 31 AF XY: 0.164 AC XY: 12165 AN XY: 74206

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.0762

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.192

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.151

Alfa AF: 0.151 Hom.: 287

Bravo AF: 0.170

Asia WGS AF: 0.241 AC: 840 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12407335; hg19: chr1-107299585;