ENST00000650850.1:n.486-5349A>G

Variant names:

• chr4-106905709-A-G
• rs440960
• ENST00000650850.1:n.486-5349A>G

Variant summary

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

The ENST00000650850.1(ENSG00000286147):​n.486-5349A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 151,988 control chromosomes in the GnomAD database, including 8,499 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 0.33 (8499 hom., cov: 32)
• Consequence: ENSG00000286147 ENST00000650850.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.249
• Publications: 5 publications found

Genes affected

ENSG00000286147 (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 (AFR) allele frequency at 95% confidence interval = 0.436 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
ENSG00000286147	ENST00000650850.1	n.486-5349A>G		intron_variant	Intron 6 of 10

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49424 AN: 151872 Hom.: 8478 Cov.: 32

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.326 AC: 49495 AN: 151988 Hom.: 8499 Cov.: 32 AF XY: 0.320 AC XY: 23765 AN XY: 74292

African (AFR) AF: 0.442 AC: 18304 AN: 41434

American (AMR) AF: 0.228 AC: 3480 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1053 AN: 3468

East Asian (EAS) AF: 0.252 AC: 1302 AN: 5166

South Asian (SAS) AF: 0.216 AC: 1040 AN: 4814

European-Finnish (FIN) AF: 0.294 AC: 3106 AN: 10570

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.298 AC: 20246 AN: 67964

Other (OTH) AF: 0.307 AC: 649 AN: 2112

Alfa AF: 0.332 Hom.: 1169

Bravo AF: 0.321

Asia WGS AF: 0.236 AC: 821 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.3
DANN	Benign	0.84
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs440960; hg19: chr4-107826866;