1-27222166-C-T

Variant names:

• chr1-27222166-C-T
• rs11247626

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 0.274 in 152,026 control chromosomes in the GnomAD database, including 6,994 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 0.27 (6994 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.138

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.741 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: 0.274 AC: 41664 AN: 151908 Hom.: 6982 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.761

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.274 AC: 41690 AN: 152026 Hom.: 6994 Cov.: 32 AF XY: 0.281 AC XY: 20849 AN XY: 74318

Gnomad4 AFR AF: 0.167

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.761

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.330

Gnomad4 NFE AF: 0.259

Gnomad4 OTH AF: 0.297

Alfa AF: 0.271 Hom.: 8112

Bravo AF: 0.284

Asia WGS AF: 0.464 AC: 1614 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11247626; hg19: chr1-27548657;