11-34680819-C-T

Position:

• chr11-34680819-C-T

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 0.195 in 152,068 control chromosomes in the GnomAD database, including 3,089 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 0.19 (3089 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129

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 (AMR) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29608 AN: 151950 Hom.: 3085 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.195 AC: 29644 AN: 152068 Hom.: 3089 Cov.: 32 AF XY: 0.196 AC XY: 14543 AN XY: 74334

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.197

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.211

Alfa AF: 0.205 Hom.: 323

Bravo AF: 0.206

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs704737; hg19: chr11-34702366;