11-67572065-T-A

Position:

• chr11-67572065-T-A

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 0.895 in 152,184 control chromosomes in the GnomAD database, including 61,028 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 0.90 (61028 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.197

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.911 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: 0.895 AC: 136160 AN: 152066 Hom.: 61008 Cov.: 32

Gnomad AFR AF: 0.871

Gnomad AMI AF: 0.940

Gnomad AMR AF: 0.894

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 0.872

Gnomad SAS AF: 0.922

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.917

Gnomad OTH AF: 0.903

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

GnomAD4 genome AF: 0.895 AC: 136235 AN: 152184 Hom.: 61028 Cov.: 32 AF XY: 0.893 AC XY: 66465 AN XY: 74392

Gnomad4 AFR AF: 0.871

Gnomad4 AMR AF: 0.894

Gnomad4 ASJ AF: 0.910

Gnomad4 EAS AF: 0.871

Gnomad4 SAS AF: 0.921

Gnomad4 FIN AF: 0.839

Gnomad4 NFE AF: 0.917

Gnomad4 OTH AF: 0.902

Alfa AF: 0.904 Hom.: 7726

Bravo AF: 0.898

Asia WGS AF: 0.900 AC: 3133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs676653; hg19: chr11-67339536;