4-147080420-A-G

Variant names:

• chr4-147080420-A-G
• rs10212894
• ENST00000667105.1:n.515+7194A>G

Variant summary

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

The ENST00000667105.1(ENSG00000286371):​n.515+7194A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.697 in 151,998 control chromosomes in the GnomAD database, including 37,560 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 0.70 (37560 hom., cov: 31)
• Consequence: ENSG00000286371 ENST00000667105.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 1 publications found

Genes affected

ENSG00000286371 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.773 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000667105.1. 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
	ENSG00000286371	ENST00000667105.1		n.515+7194A>G		intron	N/A
	ENSG00000286371	ENST00000671296.1		n.412+7194A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.697 AC: 105858 AN: 151880 Hom.: 37536 Cov.: 31

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.761

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.778

Gnomad OTH AF: 0.681

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

GnomAD4 genome AF: 0.697 AC: 105924 AN: 151998 Hom.: 37560 Cov.: 31 AF XY: 0.695 AC XY: 51629 AN XY: 74296

African (AFR) AF: 0.580 AC: 24029 AN: 41412

American (AMR) AF: 0.678 AC: 10367 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.621 AC: 2156 AN: 3472

East Asian (EAS) AF: 0.581 AC: 3002 AN: 5168

South Asian (SAS) AF: 0.679 AC: 3264 AN: 4810

European-Finnish (FIN) AF: 0.748 AC: 7907 AN: 10572

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.778 AC: 52892 AN: 67970

Other (OTH) AF: 0.679 AC: 1428 AN: 2102

Alfa AF: 0.739 Hom.: 136483

Bravo AF: 0.682

Asia WGS AF: 0.624 AC: 2171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.28
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs10212894; hg19: chr4-148001572;