chr4-99157594-C-A

Position:

• chr4-99157594-C-A

Variant summary

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

The ENST00000500358.6(ENSG00000246090):​n.3714+15C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.889 in 152,216 control chromosomes in the GnomAD database, including 60,679 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 0.89 (60679 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000246090 ENST00000500358.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.111

Genes affected

ENSG00000246090 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100507053	NR_037884.1	n.3714+15C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000246090	ENST00000500358.6	n.3714+15C>A		intron_variant		1
ADH4	ENST00000504581.1	n.169+30G>T		intron_variant		3
ENSG00000246090	ENST00000661393.1	n.765+15C>A		intron_variant
ENSG00000246090	ENST00000691990.1	n.535+15C>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.889 AC: 135177 AN: 152098 Hom.: 60652 Cov.: 32

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.978

Gnomad AMR AF: 0.926

Gnomad ASJ AF: 0.963

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.968

Gnomad FIN AF: 0.909

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.941

Gnomad OTH AF: 0.916

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.889 AC: 135253 AN: 152216 Hom.: 60679 Cov.: 32 AF XY: 0.890 AC XY: 66230 AN XY: 74404

Gnomad4 AFR AF: 0.750

Gnomad4 AMR AF: 0.926

Gnomad4 ASJ AF: 0.963

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.969

Gnomad4 FIN AF: 0.909

Gnomad4 NFE AF: 0.941

Gnomad4 OTH AF: 0.917

Alfa AF: 0.901 Hom.: 3031

Bravo AF: 0.881

Asia WGS AF: 0.961 AC: 3342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.4
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7678890; hg19: chr4-100078751;