ENST00000500358.6:n.3789+16714C>A

Variant names:

• chr4-99221145-C-A
• rs10008281
• ENST00000500358.6:n.3789+16714C>A

Variant summary

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

The ENST00000500358.6(ENSG00000246090):​n.3789+16714C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 151,978 control chromosomes in the GnomAD database, including 6,092 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 0.26 (6092 hom., cov: 32)
• Consequence: ENSG00000246090 ENST00000500358.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.799
• Publications: 11 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.756 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.3789+16714C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000246090	ENST00000500358.6	TSL:1	n.3789+16714C>A		intron	N/A
	ENSG00000246090	ENST00000506160.1	TSL:4	n.407+16714C>A		intron	N/A
	ENSG00000246090	ENST00000506454.2	TSL:3	n.168+16718C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39835 AN: 151862 Hom.: 6097 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.262 AC: 39827 AN: 151978 Hom.: 6092 Cov.: 32 AF XY: 0.263 AC XY: 19535 AN XY: 74304

African (AFR) AF: 0.283 AC: 11713 AN: 41438

American (AMR) AF: 0.195 AC: 2968 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 871 AN: 3470

East Asian (EAS) AF: 0.777 AC: 4010 AN: 5164

South Asian (SAS) AF: 0.442 AC: 2129 AN: 4820

European-Finnish (FIN) AF: 0.146 AC: 1539 AN: 10558

Middle Eastern (MID) AF: 0.277 AC: 81 AN: 292

European-Non Finnish (NFE) AF: 0.231 AC: 15732 AN: 67958

Other (OTH) AF: 0.254 AC: 537 AN: 2112

Alfa AF: 0.244 Hom.: 6160

Bravo AF: 0.264

Asia WGS AF: 0.469 AC: 1626 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.35
DANN	Benign	0.33
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs10008281; hg19: chr4-100142302;