chr1-208528320-C-T

Position:

• chr1-208528320-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0712 in 152,260 control chromosomes in the GnomAD database, including 808 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 0.071 (808 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.89

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0711 AC: 10824 AN: 152142 Hom.: 805 Cov.: 33

Gnomad AFR AF: 0.0173

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.0816

Gnomad ASJ AF: 0.0372

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.0780

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0704

Gnomad OTH AF: 0.0645

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

GnomAD4 genome AF: 0.0712 AC: 10838 AN: 152260 Hom.: 808 Cov.: 33 AF XY: 0.0744 AC XY: 5542 AN XY: 74446

Gnomad4 AFR AF: 0.0172

Gnomad4 AMR AF: 0.0822

Gnomad4 ASJ AF: 0.0372

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.0780

Gnomad4 NFE AF: 0.0704

Gnomad4 OTH AF: 0.0667

Alfa AF: 0.0671 Hom.: 444

Bravo AF: 0.0713

Asia WGS AF: 0.260 AC: 904 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	15
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12069004; hg19: chr1-208701665;