4-116928293-G-T

Variant names:

• chr4-116928293-G-T
• rs2389339
• ENST00000654940.1:n.221+28C>A

Variant summary

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

The ENST00000654940.1(ENSG00000287290):​n.221+28C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 137,682 control chromosomes in the GnomAD database, including 2,002 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 0.17 (2002 hom., cov: 29)
• Consequence: ENSG00000287290 ENST00000654940.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.447
• Publications: 2 publications found

Genes affected

ENSG00000287290 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654940.1. 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
	ENSG00000287290	ENST00000654940.1		n.221+28C>A		intron	N/A
	ENSG00000287290	ENST00000824997.1		n.596+28C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.168 AC: 23170 AN: 137586 Hom.: 2000 Cov.: 29

Gnomad AFR AF: 0.0985

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.168 AC: 23171 AN: 137682 Hom.: 2002 Cov.: 29 AF XY: 0.167 AC XY: 11172 AN XY: 66858

African (AFR) AF: 0.0984 AC: 3369 AN: 34230

American (AMR) AF: 0.172 AC: 2413 AN: 14058

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 548 AN: 3262

East Asian (EAS) AF: 0.122 AC: 579 AN: 4748

South Asian (SAS) AF: 0.118 AC: 512 AN: 4352

European-Finnish (FIN) AF: 0.194 AC: 1828 AN: 9440

Middle Eastern (MID) AF: 0.245 AC: 69 AN: 282

European-Non Finnish (NFE) AF: 0.208 AC: 13398 AN: 64484

Other (OTH) AF: 0.181 AC: 352 AN: 1942

Alfa AF: 0.0827 Hom.: 125

Bravo AF: 0.150

Asia WGS AF: 0.0910 AC: 316 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.3
DANN	Benign	0.54
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs2389339; hg19: chr4-117849449;