chr1-26498625-C-T

Position:

• chr1-26498625-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 0.31 in 151,958 control chromosomes in the GnomAD database, including 8,612 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 (8612 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.838

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.26498625C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47044 AN: 151840 Hom.: 8609 Cov.: 31

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.723

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.310 AC: 47072 AN: 151958 Hom.: 8612 Cov.: 31 AF XY: 0.314 AC XY: 23331 AN XY: 74250

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.722

Gnomad4 SAS AF: 0.424

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.297

Alfa AF: 0.244 Hom.: 2459

Bravo AF: 0.320

Asia WGS AF: 0.543 AC: 1888 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.86
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4659444; hg19: chr1-26825116;