rs12386601

chr7-92528572-A-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The variant allele was found at a frequency of 0.118 in 1,317,404 control chromosomes in the GnomAD database, including 9,581 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.12 (1163 hom., cov: 32)
  • Exomes 𝑓: 0.12 (8418 hom.)
• Consequence: Unknown
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:5
• Conservation: PhyloP100: -1.65

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 7-92528572-A-G is Benign according to our data. Variant chr7-92528572-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 256215.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.132 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: 0.121 AC: 18416 AN: 151832 Hom.: 1158 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.0782

Gnomad AMR AF: 0.0810

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.0415

Gnomad SAS AF: 0.0882

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.118

GnomAD4 exome AF: 0.117 AC: 136454 AN: 1165458 Hom.: 8418 Cov.: 17 AF XY: 0.116 AC XY: 66043 AN XY: 568846

Gnomad4 AFR exome AF: 0.136

Gnomad4 AMR exome AF: 0.0795

Gnomad4 ASJ exome AF: 0.0992

Gnomad4 EAS exome AF: 0.0410

Gnomad4 SAS exome AF: 0.0961

Gnomad4 FIN exome AF: 0.145

Gnomad4 NFE exome AF: 0.121

Gnomad4 OTH exome AF: 0.113

GnomAD4 genome AF: 0.121 AC: 18447 AN: 151946 Hom.: 1163 Cov.: 32 AF XY: 0.121 AC XY: 8993 AN XY: 74286

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.0806

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.0418

Gnomad4 SAS AF: 0.0879

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.117

Alfa AF: 0.123 Hom.: 1142

Bravo AF: 0.115

Asia WGS AF: 0.0940 AC: 328 AN: 3476

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Zellweger spectrum disorders Benign:2

Benign, no assertion criteria provided	clinical testing	Natera, Inc.	Sep 16, 2020	- -
Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 22, 2024	- -

not specified Benign:1

Likely benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

-

- -

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 18, 2021

- -

Peroxisome biogenesis disorder 1A (Zellweger) Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 01, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	1.5
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12386601; hg19: chr7-92157886;