chr1-182590375-C-T

Position:

• chr1-182590375-C-T

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 0.314 in 152,022 control chromosomes in the GnomAD database, including 8,789 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 0.31 (8789 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.339

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 = 0.436 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47750 AN: 151904 Hom.: 8789 Cov.: 31

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.314 AC: 47763 AN: 152022 Hom.: 8789 Cov.: 31 AF XY: 0.317 AC XY: 23514 AN XY: 74270

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.445

Gnomad4 ASJ AF: 0.519

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.435

Gnomad4 FIN AF: 0.351

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.367

Alfa AF: 0.378 Hom.: 23009

Bravo AF: 0.311

Asia WGS AF: 0.329 AC: 1144 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	4.0
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs682585; hg19: chr1-182559510;