chr1-106793679-G-T

Variant names:

• chr1-106793679-G-T
• rs12097821

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 22 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.284 AC: 11775 AN: 41488

American (AMR) AF: 0.157 AC: 2390 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0784 AC: 272 AN: 3468

East Asian (EAS) AF: 0.281 AC: 1451 AN: 5170

South Asian (SAS) AF: 0.191 AC: 921 AN: 4826

European-Finnish (FIN) AF: 0.148 AC: 1559 AN: 10562

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9147 AN: 67998

Other (OTH) AF: 0.163 AC: 343 AN: 2110

Alfa AF: 0.150 Hom.: 5757

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
PhyloP100		0.028

Splicing

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

Other links and lift over

dbSNP: rs12097821; hg19: chr1-107336301;