11-69258332-T-G

Position:

• chr11-69258332-T-G

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 0.761 in 152,076 control chromosomes in the GnomAD database, including 45,202 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 0.76 (45202 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.420

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.929 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: 0.761 AC: 115669 AN: 151958 Hom.: 45136 Cov.: 31

Gnomad AFR AF: 0.937

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.756

Gnomad ASJ AF: 0.721

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.686

Gnomad OTH AF: 0.748

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

GnomAD4 genome AF: 0.761 AC: 115794 AN: 152076 Hom.: 45202 Cov.: 31 AF XY: 0.763 AC XY: 56690 AN XY: 74334

Gnomad4 AFR AF: 0.937

Gnomad4 AMR AF: 0.756

Gnomad4 ASJ AF: 0.721

Gnomad4 EAS AF: 0.604

Gnomad4 SAS AF: 0.591

Gnomad4 FIN AF: 0.750

Gnomad4 NFE AF: 0.686

Gnomad4 OTH AF: 0.746

Alfa AF: 0.703 Hom.: 40336

Bravo AF: 0.773

Asia WGS AF: 0.674 AC: 2341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.85
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3884627; hg19: chr11-69025799;