3-27723132-A-G

Variant names:

• chr3-27723132-A-G
• rs3806624

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178
• Publications: 64 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.828 AC: 34277 AN: 41416

American (AMR) AF: 0.663 AC: 10125 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1818 AN: 3466

East Asian (EAS) AF: 0.830 AC: 4265 AN: 5140

South Asian (SAS) AF: 0.760 AC: 3651 AN: 4804

European-Finnish (FIN) AF: 0.487 AC: 5120 AN: 10524

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.462 AC: 31339 AN: 67902

Other (OTH) AF: 0.580 AC: 1215 AN: 2096

Alfa AF: 0.515 Hom.: 95059

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
PhyloP100		-0.18
PromoterAI		0.0088	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3806624; hg19: chr3-27764623;