4-99113846-A-G

Position:

• chr4-99113846-A-G

Variant summary

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

The ENST00000500358.6(ENSG00000246090):​n.429-19709A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.789 in 152,178 control chromosomes in the GnomAD database, including 47,912 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 0.79 (47912 hom., cov: 31)
• Consequence: ENSG00000246090 ENST00000500358.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.467

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 (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100507053	NR_037884.1	n.429-19709A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000246090	ENST00000500358.6	n.429-19709A>G		intron_variant		1
ENSG00000246090	ENST00000661393.1	n.426-19709A>G		intron_variant
ENSG00000246090	ENST00000670724.1	n.481-19709A>G		intron_variant
ENSG00000246090	ENST00000691990.1	n.446+24562A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.789 AC: 119917 AN: 152060 Hom.: 47860 Cov.: 31

Gnomad AFR AF: 0.876

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.798

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.884

Gnomad FIN AF: 0.774

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.759

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

GnomAD4 genome AF: 0.789 AC: 120030 AN: 152178 Hom.: 47912 Cov.: 31 AF XY: 0.796 AC XY: 59254 AN XY: 74402

Gnomad4 AFR AF: 0.876

Gnomad4 AMR AF: 0.798

Gnomad4 ASJ AF: 0.698

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.884

Gnomad4 FIN AF: 0.774

Gnomad4 NFE AF: 0.720

Gnomad4 OTH AF: 0.762

Alfa AF: 0.755 Hom.: 5456

Bravo AF: 0.795

Asia WGS AF: 0.931 AC: 3237 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	2.2
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2602866; hg19: chr4-100034997;