11-89177755-C-A

Position:

• chr11-89177755-C-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 0.138 in 614,940 control chromosomes in the GnomAD database, including 6,858 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.16 (2448 hom., cov: 32)
  • Exomes 𝑓: 0.13 (4410 hom.)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:2 O:1
• Conservation: PhyloP100: -0.278

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.27 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: 0.164 AC: 24948 AN: 151944 Hom.: 2430 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.171

GnomAD4 exome AF: 0.130 AC: 59995 AN: 462876 Hom.: 4410 Cov.: 5 AF XY: 0.134 AC XY: 32686 AN XY: 244832

Gnomad4 AFR exome AF: 0.273

Gnomad4 AMR exome AF: 0.132

Gnomad4 ASJ exome AF: 0.116

Gnomad4 EAS exome AF: 0.141

Gnomad4 SAS exome AF: 0.205

Gnomad4 FIN exome AF: 0.164

Gnomad4 NFE exome AF: 0.105

Gnomad4 OTH exome AF: 0.135

GnomAD4 genome AF: 0.164 AC: 25008 AN: 152064 Hom.: 2448 Cov.: 32 AF XY: 0.167 AC XY: 12415 AN XY: 74342

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.174

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.176

Alfa AF: 0.0831 Hom.: 140

Bravo AF: 0.166

ClinVar

Significance: Benign

Submissions summary: Benign:2 Other:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1 Other:1

not provided, no classification provided	literature only	Retina International	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 15, 2021	- -

Tyrosinase-negative oculocutaneous albinism Benign:1

Benign, no assertion criteria provided

literature only

OMIM

Jan 01, 1993

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.8
DANN	Benign	0.62

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1799989; hg19: chr11-88910923;