4-99293007-A-G

Position:

• chr4-99293007-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000500358.6(ENSG00000246090):​n.4160+2059A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.811 in 152,202 control chromosomes in the GnomAD database, including 50,098 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 0.81 (50098 hom., cov: 33)
• Consequence: ENSG00000246090 ENST00000500358.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.397

Genes affected

ENSG00000246090 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100507053	NR_037884.1	n.4160+2059A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000246090	ENST00000500358.6	n.4160+2059A>G		intron_variant		1
ENSG00000246090	ENST00000509939.1	n.70+2002A>G		intron_variant		3
ENSG00000246090	ENST00000661393.1	n.1268+2002A>G		intron_variant
ENSG00000246090	ENST00000691990.1	n.1038+2002A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.811 AC: 123314 AN: 152084 Hom.: 50054 Cov.: 33

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.816

Gnomad ASJ AF: 0.844

Gnomad EAS AF: 0.911

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.799

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.829

Gnomad OTH AF: 0.826

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

GnomAD4 genome AF: 0.811 AC: 123411 AN: 152202 Hom.: 50098 Cov.: 33 AF XY: 0.808 AC XY: 60138 AN XY: 74410

Gnomad4 AFR AF: 0.770

Gnomad4 AMR AF: 0.816

Gnomad4 ASJ AF: 0.844

Gnomad4 EAS AF: 0.911

Gnomad4 SAS AF: 0.764

Gnomad4 FIN AF: 0.799

Gnomad4 NFE AF: 0.829

Gnomad4 OTH AF: 0.822

Alfa AF: 0.805 Hom.: 4650

Bravo AF: 0.812

Asia WGS AF: 0.768 AC: 2669 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.9
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs904092; hg19: chr4-100214164;