chr4-99296626-G-A

Variant names:

• chr4-99296626-G-A
• rs1587264
• ENST00000500358.6:n.4161-3673G>A

Variant summary

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

The ENST00000500358.6(ENSG00000246090):​n.4161-3673G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.771 in 152,052 control chromosomes in the GnomAD database, including 45,351 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 0.77 (45351 hom., cov: 33)
• Consequence: ENSG00000246090 ENST00000500358.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.545
• Publications: 1 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.889 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC100507053	NR_037884.1		n.4161-3673G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000246090	ENST00000500358.6	TSL:1	n.4161-3673G>A		intron	N/A
	ENSG00000246090	ENST00000509939.1	TSL:3	n.71-3673G>A		intron	N/A
	ENSG00000246090	ENST00000661393.1		n.1269-3673G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.771 AC: 117211 AN: 151936 Hom.: 45313 Cov.: 33

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.805

Gnomad EAS AF: 0.910

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.788

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

GnomAD4 genome AF: 0.771 AC: 117302 AN: 152052 Hom.: 45351 Cov.: 33 AF XY: 0.768 AC XY: 57090 AN XY: 74328

African (AFR) AF: 0.726 AC: 30116 AN: 41496

American (AMR) AF: 0.764 AC: 11661 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.805 AC: 2793 AN: 3468

East Asian (EAS) AF: 0.910 AC: 4718 AN: 5182

South Asian (SAS) AF: 0.709 AC: 3418 AN: 4820

European-Finnish (FIN) AF: 0.745 AC: 7868 AN: 10568

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.796 AC: 54045 AN: 67938

Other (OTH) AF: 0.784 AC: 1654 AN: 2110

Alfa AF: 0.785 Hom.: 5819

Bravo AF: 0.771

Asia WGS AF: 0.729 AC: 2534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.3
DANN	Benign	0.71
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs1587264; hg19: chr4-100217783;