chr3-127181649-T-C

Position:

• chr3-127181649-T-C

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 0.443 in 152,126 control chromosomes in the GnomAD database, including 15,329 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 0.44 (15329 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.873

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.127181649T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287784	ENST00000654542.1	n.85-14853A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67278 AN: 152008 Hom.: 15313 Cov.: 33

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.443 AC: 67336 AN: 152126 Hom.: 15329 Cov.: 33 AF XY: 0.443 AC XY: 32910 AN XY: 74348

Gnomad4 AFR AF: 0.368

Gnomad4 AMR AF: 0.409

Gnomad4 ASJ AF: 0.544

Gnomad4 EAS AF: 0.583

Gnomad4 SAS AF: 0.626

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.476

Gnomad4 OTH AF: 0.452

Alfa AF: 0.474 Hom.: 10208

Bravo AF: 0.435

Asia WGS AF: 0.630 AC: 2195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.5
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9827714; hg19: chr3-126900492;