chr4-99242716-G-A

Position:

• chr4-99242716-G-A

Variant summary

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

The ENST00000500358.6(ENSG00000246090):​n.3789+38285G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 151,986 control chromosomes in the GnomAD database, including 12,111 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 0.38 (12111 hom., cov: 32)
• Consequence: ENSG00000246090 ENST00000500358.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.741

Genes affected

ENSG00000246090 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.492 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100507053	NR_037884.1	n.3789+38285G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000246090	ENST00000500358.6	n.3789+38285G>A		intron_variant		1
ENSG00000246090	ENST00000506160.1	n.408-35737G>A		intron_variant		4
ENSG00000246090	ENST00000506454.1	n.167-10119G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56963 AN: 151866 Hom.: 12109 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.375 AC: 56996 AN: 151986 Hom.: 12111 Cov.: 32 AF XY: 0.373 AC XY: 27711 AN XY: 74284

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.501

Gnomad4 ASJ AF: 0.544

Gnomad4 EAS AF: 0.133

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.481

Gnomad4 NFE AF: 0.465

Gnomad4 OTH AF: 0.426

Alfa AF: 0.291 Hom.: 766

Bravo AF: 0.371

Asia WGS AF: 0.222 AC: 774 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.82
DANN	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2201728; hg19: chr4-100163873;