rs13228827

Positions:

• chr7-33062902-G-A
• chr7-33062902-G-C
• chr7-33062902-G-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The variant allele was found at a frequency of 0.705 in 969,208 control chromosomes in the GnomAD database, including 242,739 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.73 (40222 hom., cov: 33)
  • Exomes 𝑓: 0.70 (202517 hom.)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.438

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 7-33062902-G-A is Benign according to our data. Variant chr7-33062902-G-A is described in ClinVar as [Benign]. Clinvar id is 1295988.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.781 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: 0.725 AC: 110115 AN: 151860 Hom.: 40175 Cov.: 33

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.618

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.696

GnomAD4 exome AF: 0.702 AC: 573380 AN: 817230 Hom.: 202517 AF XY: 0.698 AC XY: 293330 AN XY: 420454

Gnomad4 AFR exome AF: 0.805

Gnomad4 AMR exome AF: 0.799

Gnomad4 ASJ exome AF: 0.570

Gnomad4 EAS exome AF: 0.648

Gnomad4 SAS exome AF: 0.636

Gnomad4 FIN exome AF: 0.758

Gnomad4 NFE exome AF: 0.705

Gnomad4 OTH exome AF: 0.686

GnomAD4 genome AF: 0.725 AC: 110220 AN: 151978 Hom.: 40222 Cov.: 33 AF XY: 0.727 AC XY: 53975 AN XY: 74292

Gnomad4 AFR AF: 0.788

Gnomad4 AMR AF: 0.748

Gnomad4 ASJ AF: 0.568

Gnomad4 EAS AF: 0.630

Gnomad4 SAS AF: 0.623

Gnomad4 FIN AF: 0.760

Gnomad4 NFE AF: 0.703

Gnomad4 OTH AF: 0.693

Alfa AF: 0.653 Hom.: 2147

Bravo AF: 0.726

Asia WGS AF: 0.628 AC: 2184 AN: 3472

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.5
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13228827; hg19: chr7-33102514;