1-111017226-G-T

Variant names:

• chr1-111017226-G-T
• rs12735344

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 0.208 in 152,052 control chromosomes in the GnomAD database, including 3,542 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 0.21 (3542 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.25 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: 0.208 AC: 31640 AN: 151934 Hom.: 3543 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.00404

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.208 AC: 31651 AN: 152052 Hom.: 3542 Cov.: 32 AF XY: 0.204 AC XY: 15137 AN XY: 74332

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.00405

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.205

Alfa AF: 0.234 Hom.: 6248

Bravo AF: 0.197

Asia WGS AF: 0.0880 AC: 305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.0
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12735344; hg19: chr1-111559848;