1-17452075-T-G

Variant names:

• chr1-17452075-T-G
• rs2526822

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.403 in 151,826 control chromosomes in the GnomAD database, including 13,048 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 0.40 (13048 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.63
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.521 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: 0.403 AC: 61140 AN: 151708 Hom.: 13021 Cov.: 31

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.403 AC: 61220 AN: 151826 Hom.: 13048 Cov.: 31 AF XY: 0.409 AC XY: 30314 AN XY: 74174

African (AFR) AF: 0.527 AC: 21811 AN: 41400

American (AMR) AF: 0.276 AC: 4211 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 898 AN: 3470

East Asian (EAS) AF: 0.353 AC: 1815 AN: 5148

South Asian (SAS) AF: 0.407 AC: 1957 AN: 4812

European-Finnish (FIN) AF: 0.475 AC: 5000 AN: 10520

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.360 AC: 24444 AN: 67916

Other (OTH) AF: 0.391 AC: 826 AN: 2110

Alfa AF: 0.366 Hom.: 38199

Bravo AF: 0.394

Asia WGS AF: 0.379 AC: 1318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.025
DANN	Benign	0.79
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs2526822; hg19: chr1-17778571;