rs4699718

Positions:

• chr4-99146639-G-A
• chr4-99146639-G-T

Variant summary

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

The ENST00000500358.6(ENSG00000246090):​n.680-7906G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 151,982 control chromosomes in the GnomAD database, including 3,972 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 0.21 (3972 hom., cov: 32)
• Consequence: ENSG00000246090 ENST00000500358.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104

Genes affected

ENSG00000246090 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100507053	NR_037884.1	n.680-7906G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000246090	ENST00000500358.6	n.680-7906G>A		intron_variant		1
ADH4	ENST00000504581.1	n.170-3859C>T		intron_variant		3
ENSG00000246090	ENST00000661393.1	n.677-10852G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31762 AN: 151864 Hom.: 3973 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.209 AC: 31768 AN: 151982 Hom.: 3972 Cov.: 32 AF XY: 0.202 AC XY: 14979 AN XY: 74258

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.299

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.282

Gnomad4 OTH AF: 0.236

Alfa AF: 0.238 Hom.: 598

Bravo AF: 0.202

Asia WGS AF: 0.0680 AC: 237 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.85
DANN	Benign	0.11

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4699718; hg19: chr4-100067791;