1-111289601-T-C

Position:

• chr1-111289601-T-C

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 0.258 in 152,156 control chromosomes in the GnomAD database, including 5,455 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 0.26 (5455 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700

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 (AFR) allele frequency at 95% confidence interval = 0.342 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: 0.258 AC: 39218 AN: 152038 Hom.: 5455 Cov.: 33

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.0906

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.258 AC: 39240 AN: 152156 Hom.: 5455 Cov.: 33 AF XY: 0.257 AC XY: 19149 AN XY: 74398

Gnomad4 AFR AF: 0.347

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.240

Gnomad4 EAS AF: 0.0906

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.225

Alfa AF: 0.241 Hom.: 2500

Bravo AF: 0.253

Asia WGS AF: 0.171 AC: 598 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	1.5
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10494132; hg19: chr1-111832223;