11-36977835-C-T

Variant names:

• chr11-36977835-C-T
• rs1871684

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 0.344 in 151,800 control chromosomes in the GnomAD database, including 10,296 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 0.34 (10296 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0990

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.465 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: 0.344 AC: 52113 AN: 151682 Hom.: 10285 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.344 AC: 52145 AN: 151800 Hom.: 10296 Cov.: 32 AF XY: 0.352 AC XY: 26073 AN XY: 74158

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.457

Gnomad4 ASJ AF: 0.432

Gnomad4 EAS AF: 0.481

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.533

Gnomad4 NFE AF: 0.399

Gnomad4 OTH AF: 0.337

Alfa AF: 0.383 Hom.: 19336

Bravo AF: 0.330

Asia WGS AF: 0.356 AC: 1237 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.6
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1871684; hg19: chr11-36999385;