1-207495285-C-T

Variant names:

• chr1-207495285-C-T
• rs9429942

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 0.644 in 151,260 control chromosomes in the GnomAD database, including 32,344 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 0.64 (32344 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.936 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: 0.644 AC: 97333 AN: 151140 Hom.: 32345 Cov.: 28

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.672

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.684

Gnomad EAS AF: 0.958

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.689

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.650

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

GnomAD4 genome AF: 0.644 AC: 97352 AN: 151260 Hom.: 32344 Cov.: 28 AF XY: 0.652 AC XY: 48155 AN XY: 73892

Gnomad4 AFR AF: 0.481

Gnomad4 AMR AF: 0.723

Gnomad4 ASJ AF: 0.684

Gnomad4 EAS AF: 0.958

Gnomad4 SAS AF: 0.825

Gnomad4 FIN AF: 0.718

Gnomad4 NFE AF: 0.673

Gnomad4 OTH AF: 0.652

Alfa AF: 0.642 Hom.: 3794

Bravo AF: 0.640

Asia WGS AF: 0.858 AC: 2981 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.67
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9429942; hg19: chr1-207668630;