rs6819724

Variant names:

• chr4-99107300-A-G
• rs6819724
• ENST00000500358.6:n.428+18016A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000500358.6(ENSG00000246090):​n.428+18016A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0847 in 152,096 control chromosomes in the GnomAD database, including 981 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 0.085 (981 hom., cov: 32)
• Consequence: ENSG00000246090 ENST00000500358.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 3 publications found

Genes affected

ENSG00000246090 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100507053	NR_037884.1	n.428+18016A>G		intron_variant	Intron 1 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000246090	ENST00000500358.6	n.428+18016A>G		intron_variant	Intron 1 of 9	1
ENSG00000246090	ENST00000661393.1	n.425+18016A>G		intron_variant	Intron 1 of 9
ENSG00000246090	ENST00000670724.2	n.480+18016A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0847 AC: 12865 AN: 151978 Hom.: 978 Cov.: 32

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0430

Gnomad ASJ AF: 0.0222

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0149

Gnomad FIN AF: 0.0414

Gnomad MID AF: 0.0577

Gnomad NFE AF: 0.0392

Gnomad OTH AF: 0.0679

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

GnomAD4 genome AF: 0.0847 AC: 12890 AN: 152096 Hom.: 981 Cov.: 32 AF XY: 0.0826 AC XY: 6141 AN XY: 74370

African (AFR) AF: 0.212 AC: 8808 AN: 41462

American (AMR) AF: 0.0429 AC: 656 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0222 AC: 77 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5178

South Asian (SAS) AF: 0.0147 AC: 71 AN: 4818

European-Finnish (FIN) AF: 0.0414 AC: 439 AN: 10592

Middle Eastern (MID) AF: 0.0586 AC: 17 AN: 290

European-Non Finnish (NFE) AF: 0.0392 AC: 2662 AN: 67982

Other (OTH) AF: 0.0672 AC: 142 AN: 2112

Alfa AF: 0.0649 Hom.: 71

Bravo AF: 0.0907

Asia WGS AF: 0.0200 AC: 70 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.7
DANN	Benign	0.43
PhyloP100		0.16
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs6819724; hg19: chr4-100028451;