ENST00000654219.1:n.191-6365C>G

Variant names:

• chr2-76378865-C-G
• rs908958
• ENST00000654219.1:n.191-6365C>G

Variant summary

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

The ENST00000654219.1(ENSG00000287172):​n.191-6365C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.795 in 152,138 control chromosomes in the GnomAD database, including 48,699 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 0.80 (48699 hom., cov: 32)
• Consequence: ENSG00000287172 ENST00000654219.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550
• Publications: 2 publications found

Genes affected

ENSG00000287172 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654219.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287172	ENST00000654219.1		n.191-6365C>G		intron	N/A
	ENSG00000287172	ENST00000668214.1		n.163-16823C>G		intron	N/A
	ENSG00000287172	ENST00000669228.1		n.191-6387C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.795 AC: 120902 AN: 152020 Hom.: 48679 Cov.: 32

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.766

Gnomad AMR AF: 0.744

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 0.679

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.813

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.871

Gnomad OTH AF: 0.821

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

GnomAD4 genome AF: 0.795 AC: 120966 AN: 152138 Hom.: 48699 Cov.: 32 AF XY: 0.793 AC XY: 58957 AN XY: 74368

African (AFR) AF: 0.687 AC: 28478 AN: 41482

American (AMR) AF: 0.744 AC: 11375 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.910 AC: 3156 AN: 3468

East Asian (EAS) AF: 0.679 AC: 3496 AN: 5146

South Asian (SAS) AF: 0.810 AC: 3902 AN: 4820

European-Finnish (FIN) AF: 0.813 AC: 8620 AN: 10602

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.871 AC: 59247 AN: 68008

Other (OTH) AF: 0.814 AC: 1720 AN: 2112

Alfa AF: 0.832 Hom.: 6302

Bravo AF: 0.783

Asia WGS AF: 0.685 AC: 2383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.60
PhyloP100		-0.055

Splicing

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

Other links and lift over

dbSNP: rs908958; hg19: chr2-76605991;