3-66909048-T-C

Variant names:

• chr3-66909048-T-C
• rs1456217
• ENST00000777942.1:n.71-29454A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000777942.1(ENSG00000288039):​n.71-29454A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.722 in 152,092 control chromosomes in the GnomAD database, including 40,605 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 0.72 (40605 hom., cov: 32)
• Consequence: ENSG00000288039 ENST00000777942.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.146
• Publications: 3 publications found

Genes affected

ENSG00000288039 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000777942.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288039	ENST00000777942.1		n.71-29454A>G		intron	N/A
	ENSG00000288039	ENST00000777943.1		n.66-29454A>G		intron	N/A
	ENSG00000288039	ENST00000777944.1		n.47-29454A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.722 AC: 109721 AN: 151974 Hom.: 40582 Cov.: 32

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.800

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.960

Gnomad SAS AF: 0.919

Gnomad FIN AF: 0.774

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.766

Gnomad OTH AF: 0.717

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

GnomAD4 genome AF: 0.722 AC: 109787 AN: 152092 Hom.: 40605 Cov.: 32 AF XY: 0.728 AC XY: 54140 AN XY: 74356

African (AFR) AF: 0.555 AC: 23032 AN: 41464

American (AMR) AF: 0.800 AC: 12238 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.706 AC: 2452 AN: 3472

East Asian (EAS) AF: 0.960 AC: 4983 AN: 5190

South Asian (SAS) AF: 0.919 AC: 4436 AN: 4826

European-Finnish (FIN) AF: 0.774 AC: 8179 AN: 10570

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.766 AC: 52077 AN: 67968

Other (OTH) AF: 0.718 AC: 1516 AN: 2112

Alfa AF: 0.752 Hom.: 47946

Bravo AF: 0.713

Asia WGS AF: 0.883 AC: 3068 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.63
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs1456217; hg19: chr3-66959472;