chr1-207016229-C-T

Variant names:

• chr1-207016229-C-T
• rs12409177

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 0.141 in 152,180 control chromosomes in the GnomAD database, including 1,702 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 0.14 (1702 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.111

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.21 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: 0.140 AC: 21342 AN: 152062 Hom.: 1688 Cov.: 32

Gnomad AFR AF: 0.0820

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.0607

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.141 AC: 21394 AN: 152180 Hom.: 1702 Cov.: 32 AF XY: 0.140 AC XY: 10445 AN XY: 74390

Gnomad4 AFR AF: 0.0825

Gnomad4 AMR AF: 0.216

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.0605

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.187

Alfa AF: 0.161 Hom.: 2046

Bravo AF: 0.141

Asia WGS AF: 0.126 AC: 437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.0
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12409177; hg19: chr1-207189574;