11-80251105-A-T

Position:

• chr11-80251105-A-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 0.0432 in 152,250 control chromosomes in the GnomAD database, including 313 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 0.043 (313 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

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 = 0.256 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: 0.0432 AC: 6569 AN: 152130 Hom.: 313 Cov.: 32

Gnomad AFR AF: 0.00835

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0396

Gnomad ASJ AF: 0.0302

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.0739

Gnomad FIN AF: 0.0869

Gnomad MID AF: 0.0255

Gnomad NFE AF: 0.0406

Gnomad OTH AF: 0.0330

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

GnomAD4 genome AF: 0.0432 AC: 6571 AN: 152250 Hom.: 313 Cov.: 32 AF XY: 0.0480 AC XY: 3574 AN XY: 74434

Gnomad4 AFR AF: 0.00832

Gnomad4 AMR AF: 0.0397

Gnomad4 ASJ AF: 0.0302

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.0742

Gnomad4 FIN AF: 0.0869

Gnomad4 NFE AF: 0.0406

Gnomad4 OTH AF: 0.0321

Alfa AF: 0.0443 Hom.: 24

Bravo AF: 0.0420

Asia WGS AF: 0.143 AC: 497 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.064
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11231991; hg19: chr11-79962149;