1-111289669-T-C

Variant names:

• chr1-111289669-T-C
• rs3806446

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 0.42 in 152,006 control chromosomes in the GnomAD database, including 14,486 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 0.42 (14486 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.65
• Publications: 14 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 (EAS) allele frequency at 95% confidence interval = 0.71 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: 0.420 AC: 63806 AN: 151888 Hom.: 14478 Cov.: 31

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.730

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.420 AC: 63843 AN: 152006 Hom.: 14486 Cov.: 31 AF XY: 0.424 AC XY: 31461 AN XY: 74278

African (AFR) AF: 0.280 AC: 11600 AN: 41472

American (AMR) AF: 0.599 AC: 9153 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1822 AN: 3470

East Asian (EAS) AF: 0.730 AC: 3753 AN: 5144

South Asian (SAS) AF: 0.420 AC: 2023 AN: 4816

European-Finnish (FIN) AF: 0.407 AC: 4293 AN: 10556

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.439 AC: 29830 AN: 67960

Other (OTH) AF: 0.450 AC: 949 AN: 2110

Alfa AF: 0.436 Hom.: 42673

Bravo AF: 0.436

Asia WGS AF: 0.539 AC: 1872 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	0.65
DANN	Benign	0.66
PhyloP100		-3.6

Splicing

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

Other links and lift over

dbSNP: rs3806446; hg19: chr1-111832291;