4-116928293-G-T

Position:

• chr4-116928293-G-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000287290 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986306	XR_001741796.2	n.221+28C>A		intron_variant
LOC107986306	XR_001741797.2	n.172+28C>A		intron_variant
LOC107986306	XR_001741798.2	n.221+28C>A		intron_variant
LOC107986306	XR_001741800.2	n.221+28C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287290	ENST00000654940.1	n.221+28C>A		intron_variant

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

Gnomad4 AFR AF: 0.0984

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.181

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2389339; hg19: chr4-117849449;