rs2275913

Positions:

• chr6-52186235-G-A
• chr6-52186235-G-C

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 0.284 in 152,124 control chromosomes in the GnomAD database, including 7,469 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.28 (7469 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.334

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 6-52186235-G-A is Benign according to our data. Variant chr6-52186235-G-A is described in ClinVar as [Benign]. Clinvar id is 1278437.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.45 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: 0.284 AC: 43152 AN: 152006 Hom.: 7472 Cov.: 33

Gnomad AFR AF: 0.0959

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.284 AC: 43144 AN: 152124 Hom.: 7469 Cov.: 33 AF XY: 0.291 AC XY: 21659 AN XY: 74346

Gnomad4 AFR AF: 0.0957

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.465

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.472

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.287

Alfa AF: 0.334 Hom.: 6199

Bravo AF: 0.255

Asia WGS AF: 0.372 AC: 1293 AN: 3478

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

This variant is associated with the following publications: (PMID: 22537748, 21672939, 22028838, 29372577, 25595174, 29985710, 23778030) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.8
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2275913; hg19: chr6-52051033;