rs12654778

Variant names:

• chr5-148826178-G-A
• rs12654778

Your query was ambiguous. Multiple possible variants found:

• chr5-148826178-G-A
• chr5-148826178-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Moderate BP6_Moderate BA1

The variant allele was found at a frequency of 0.345 in 155,164 control chromosomes in the GnomAD database, including 9,773 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.34 (9503 hom., cov: 31)
  • Exomes 𝑓: 0.36 (270 hom.)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.60

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BP6: Variant 5-148826178-G-A is Benign according to our data. Variant chr5-148826178-G-A is described in ClinVar as [Benign]. Clinvar id is 1180015.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52246 AN: 151672 Hom.: 9487 Cov.: 31

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.357

GnomAD4 exome AF: 0.363 AC: 1225 AN: 3374 Hom.: 270 Cov.: 0 AF XY: 0.357 AC XY: 646 AN XY: 1810

Gnomad4 AFR exome AF: 0.0556

Gnomad4 AMR exome AF: 0.324

Gnomad4 ASJ exome AF: 0.353

Gnomad4 EAS exome AF: 0.188

Gnomad4 SAS exome AF: 0.350

Gnomad4 FIN exome AF: 0.422

Gnomad4 NFE exome AF: 0.363

Gnomad4 OTH exome AF: 0.371

GnomAD4 genome AF: 0.344 AC: 52287 AN: 151790 Hom.: 9503 Cov.: 31 AF XY: 0.351 AC XY: 26058 AN XY: 74198

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.388

Gnomad4 ASJ AF: 0.415

Gnomad4 EAS AF: 0.384

Gnomad4 SAS AF: 0.390

Gnomad4 FIN AF: 0.473

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.364

Alfa AF: 0.365 Hom.: 20508

Bravo AF: 0.332

Asia WGS AF: 0.399 AC: 1383 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jan 09, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 29588580) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	16
DANN	Benign	0.89

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: rs12654778; hg19: chr5-148205741;