chr4-99273820-G-A

Variant names:

• chr4-99273820-G-A
• rs6811453
• ENST00000500358.6:n.3790-12975G>A

Variant summary

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

The ENST00000500358.6(ENSG00000246090):​n.3790-12975G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 152,112 control chromosomes in the GnomAD database, including 7,051 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 0.27 (7051 hom., cov: 32)
• Consequence: ENSG00000246090 ENST00000500358.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130
• Publications: 16 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 (NFE) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000500358.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC100507053	NR_037884.1		n.3790-12975G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000246090	ENST00000500358.6	TSL:1	n.3790-12975G>A		intron	N/A
	ENSG00000246090	ENST00000509295.5	TSL:1	n.695-305G>A		intron	N/A
	ENSG00000246090	ENST00000506160.1	TSL:4	n.408-4633G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41740 AN: 151994 Hom.: 7055 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.0257

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.274 AC: 41741 AN: 152112 Hom.: 7051 Cov.: 32 AF XY: 0.268 AC XY: 19903 AN XY: 74342

African (AFR) AF: 0.100 AC: 4170 AN: 41558

American (AMR) AF: 0.263 AC: 4014 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.462 AC: 1604 AN: 3472

East Asian (EAS) AF: 0.0257 AC: 133 AN: 5172

South Asian (SAS) AF: 0.156 AC: 753 AN: 4816

European-Finnish (FIN) AF: 0.346 AC: 3647 AN: 10544

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.385 AC: 26195 AN: 67954

Other (OTH) AF: 0.327 AC: 691 AN: 2112

Alfa AF: 0.336 Hom.: 26938

Bravo AF: 0.260

Asia WGS AF: 0.0990 AC: 346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.33
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs6811453; hg19: chr4-100194977;