rs4897612

chr6-132714186-A-C

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The variant allele was found at a frequency of 0.407 in 683,500 control chromosomes in the GnomAD database, including 64,653 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.52 (23806 hom., cov: 32)
  • Exomes 𝑓: 0.38 (40847 hom.)
• Consequence: Unknown
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: -2.25

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 6-132714186-A-C is Benign according to our data. Variant chr6-132714186-A-C is described in ClinVar as [Benign]. Clinvar id is 6230.Status of the report is no_assertion_criteria_provided, 0 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.838 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: 0.515 AC: 78327 AN: 151988 Hom.: 23755 Cov.: 32

Gnomad AFR AF: 0.845

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.508

GnomAD4 exome AF: 0.376 AC: 199819 AN: 531394 Hom.: 40847 AF XY: 0.378 AC XY: 104347 AN XY: 275692

Gnomad4 AFR exome AF: 0.841

Gnomad4 AMR exome AF: 0.563

Gnomad4 ASJ exome AF: 0.308

Gnomad4 EAS exome AF: 0.371

Gnomad4 SAS exome AF: 0.456

Gnomad4 FIN exome AF: 0.409

Gnomad4 NFE exome AF: 0.336

Gnomad4 OTH exome AF: 0.399

GnomAD4 genome AF: 0.516 AC: 78445 AN: 152106 Hom.: 23806 Cov.: 32 AF XY: 0.519 AC XY: 38596 AN XY: 74342

Gnomad4 AFR AF: 0.845

Gnomad4 AMR AF: 0.552

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.383

Gnomad4 SAS AF: 0.473

Gnomad4 FIN AF: 0.430

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.510

Alfa AF: 0.492 Hom.: 3910

Bravo AF: 0.537

Asia WGS AF: 0.512 AC: 1784 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

RECLASSIFIED - VNN1 POLYMORPHISM Benign:1

Benign, no assertion criteria provided

literature only

OMIM

Oct 01, 2007

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.34
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4897612; hg19: chr6-133035325;