3-27723132-A-G

Position:

• chr3-27723132-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.608 in 151,812 control chromosomes in the GnomAD database, including 30,316 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.61 (30316 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.82 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.27723132A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.608 AC: 92199 AN: 151694 Hom.: 30266 Cov.: 30

Gnomad AFR AF: 0.827

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.831

Gnomad SAS AF: 0.760

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.608 AC: 92309 AN: 151812 Hom.: 30316 Cov.: 30 AF XY: 0.613 AC XY: 45494 AN XY: 74192

Gnomad4 AFR AF: 0.828

Gnomad4 AMR AF: 0.663

Gnomad4 ASJ AF: 0.525

Gnomad4 EAS AF: 0.830

Gnomad4 SAS AF: 0.760

Gnomad4 FIN AF: 0.487

Gnomad4 NFE AF: 0.462

Gnomad4 OTH AF: 0.580

Alfa AF: 0.495 Hom.: 39246

Bravo AF: 0.629

Asia WGS AF: 0.803 AC: 2789 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.6
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3806624; hg19: chr3-27764623;