11-72674681-C-T

Position:

• chr11-72674681-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 0.879 in 160,224 control chromosomes in the GnomAD database, including 62,489 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 0.88 (59271 hom., cov: 28)
  • Exomes 𝑓: 0.87 (3218 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.476

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.94 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: 0.880 AC: 133489 AN: 151662 Hom.: 59228 Cov.: 28

Gnomad AFR AF: 0.948

Gnomad AMI AF: 0.919

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.856

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.852

Gnomad FIN AF: 0.857

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.889

Gnomad OTH AF: 0.868

GnomAD4 exome AF: 0.866 AC: 7310 AN: 8444 Hom.: 3218 AF XY: 0.865 AC XY: 3814 AN XY: 4408

Gnomad4 AFR exome AF: 0.965

Gnomad4 AMR exome AF: 0.698

Gnomad4 ASJ exome AF: 0.865

Gnomad4 EAS exome AF: 0.565

Gnomad4 SAS exome AF: 0.838

Gnomad4 FIN exome AF: 0.867

Gnomad4 NFE exome AF: 0.888

Gnomad4 OTH exome AF: 0.857

GnomAD4 genome AF: 0.880 AC: 133584 AN: 151780 Hom.: 59271 Cov.: 28 AF XY: 0.875 AC XY: 64920 AN XY: 74164

Gnomad4 AFR AF: 0.948

Gnomad4 AMR AF: 0.775

Gnomad4 ASJ AF: 0.856

Gnomad4 EAS AF: 0.616

Gnomad4 SAS AF: 0.852

Gnomad4 FIN AF: 0.857

Gnomad4 NFE AF: 0.889

Gnomad4 OTH AF: 0.866

Alfa AF: 0.884 Hom.: 31500

Bravo AF: 0.874

Asia WGS AF: 0.759 AC: 2641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	16
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs341058; hg19: chr11-72385725;