chr11-127969047-T-C

Variant names:

• chr11-127969047-T-C
• rs1364780

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 0.0241 in 152,202 control chromosomes in the GnomAD database, including 138 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 0.024 (138 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.410

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.165 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: 0.0241 AC: 3658 AN: 152084 Hom.: 137 Cov.: 32

Gnomad AFR AF: 0.0295

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0287

Gnomad ASJ AF: 0.0314

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.00745

Gnomad FIN AF: 0.0250

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00888

Gnomad OTH AF: 0.0301

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

GnomAD4 genome AF: 0.0241 AC: 3668 AN: 152202 Hom.: 138 Cov.: 32 AF XY: 0.0252 AC XY: 1877 AN XY: 74428

Gnomad4 AFR AF: 0.0300

Gnomad4 AMR AF: 0.0287

Gnomad4 ASJ AF: 0.0314

Gnomad4 EAS AF: 0.175

Gnomad4 SAS AF: 0.00725

Gnomad4 FIN AF: 0.0250

Gnomad4 NFE AF: 0.00889

Gnomad4 OTH AF: 0.0293

Alfa AF: 0.0131 Hom.: 5

Bravo AF: 0.0271

Asia WGS AF: 0.0850 AC: 294 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.5
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1364780; hg19: chr11-127838942;