chr1-206859406-C-T

Variant names:

• chr1-206859406-C-T
• rs574773

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 0.106 in 152,190 control chromosomes in the GnomAD database, including 1,059 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 0.11 (1059 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.154
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.316 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: 0.106 AC: 16183 AN: 152072 Hom.: 1060 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0806

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.0815

Gnomad FIN AF: 0.0829

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0811

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.106 AC: 16188 AN: 152190 Hom.: 1059 Cov.: 32 AF XY: 0.108 AC XY: 8009 AN XY: 74404

African (AFR) AF: 0.132 AC: 5476 AN: 41508

American (AMR) AF: 0.106 AC: 1629 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0806 AC: 280 AN: 3472

East Asian (EAS) AF: 0.329 AC: 1700 AN: 5168

South Asian (SAS) AF: 0.0809 AC: 390 AN: 4818

European-Finnish (FIN) AF: 0.0829 AC: 879 AN: 10602

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0811 AC: 5514 AN: 68004

Other (OTH) AF: 0.103 AC: 217 AN: 2114

Alfa AF: 0.0929 Hom.: 2966

Bravo AF: 0.112

Asia WGS AF: 0.190 AC: 659 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	16
DANN	Benign	0.69
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs574773; hg19: chr1-207032751;