ENST00000661928.1:n.104+3470A>G

Variant names:

• chr4-148449340-A-G
• rs10213471
• ENST00000661928.1:n.104+3470A>G

Variant summary

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

The ENST00000661928.1(ENSG00000287292):​n.104+3470A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.845 in 152,280 control chromosomes in the GnomAD database, including 54,480 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 0.84 (54480 hom., cov: 34)
• Consequence: ENSG00000287292 ENST00000661928.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260
• Publications: 3 publications found

Genes affected

ENSG00000287292 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.874 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
ENSG00000287292	ENST00000661928.1	n.104+3470A>G		intron_variant	Intron 1 of 3
ENSG00000287292	ENST00000669991.1	n.168+3470A>G		intron_variant	Intron 1 of 1
ENSG00000287292	ENST00000817567.1	n.249+6380A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.845 AC: 128557 AN: 152162 Hom.: 54432 Cov.: 34

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.722

Gnomad AMR AF: 0.807

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.872

Gnomad SAS AF: 0.895

Gnomad FIN AF: 0.893

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.844

Gnomad OTH AF: 0.855

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

GnomAD4 genome AF: 0.845 AC: 128661 AN: 152280 Hom.: 54480 Cov.: 34 AF XY: 0.847 AC XY: 63051 AN XY: 74454

African (AFR) AF: 0.838 AC: 34803 AN: 41546

American (AMR) AF: 0.807 AC: 12348 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.882 AC: 3063 AN: 3472

East Asian (EAS) AF: 0.871 AC: 4519 AN: 5186

South Asian (SAS) AF: 0.896 AC: 4327 AN: 4828

European-Finnish (FIN) AF: 0.893 AC: 9471 AN: 10608

Middle Eastern (MID) AF: 0.922 AC: 271 AN: 294

European-Non Finnish (NFE) AF: 0.844 AC: 57391 AN: 68016

Other (OTH) AF: 0.857 AC: 1811 AN: 2114

Alfa AF: 0.845 Hom.: 8185

Bravo AF: 0.835

Asia WGS AF: 0.889 AC: 3092 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.3
DANN	Benign	0.55
PhyloP100		0.026

Splicing

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

Other links and lift over

dbSNP: rs10213471; hg19: chr4-149370492;