chr4-99146186-A-G

Position:

• chr4-99146186-A-G

Variant summary

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

The ENST00000500358.6(ENSG00000246090):​n.680-8359A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0894 in 152,084 control chromosomes in the GnomAD database, including 942 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 0.089 (942 hom., cov: 32)
• Consequence: ENSG00000246090 ENST00000500358.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170

Genes affected

ENSG00000246090 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100507053	NR_037884.1	n.680-8359A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000246090	ENST00000500358.6	n.680-8359A>G		intron_variant		1
ADH4	ENST00000504581.1	n.170-3406T>C		intron_variant		3
ENSG00000246090	ENST00000661393.1	n.677-11305A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0894 AC: 13578 AN: 151964 Hom.: 938 Cov.: 32

Gnomad AFR AF: 0.0448

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.0806

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.0599

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0775

Gnomad OTH AF: 0.0873

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

GnomAD4 genome AF: 0.0894 AC: 13594 AN: 152084 Hom.: 942 Cov.: 32 AF XY: 0.0945 AC XY: 7024 AN XY: 74338

Gnomad4 AFR AF: 0.0447

Gnomad4 AMR AF: 0.233

Gnomad4 ASJ AF: 0.0806

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.0608

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.0775

Gnomad4 OTH AF: 0.0878

Alfa AF: 0.0879 Hom.: 987

Bravo AF: 0.100

Asia WGS AF: 0.132 AC: 458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	8.7
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2226896; hg19: chr4-100067337;