rs10008281

Positions:

• chr4-99221145-C-A
• chr4-99221145-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000246090 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100507053	NR_037884.1	n.3789+16714C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000246090	ENST00000500358.6	n.3789+16714C>A		intron_variant		1
ENSG00000246090	ENST00000506160.1	n.407+16714C>A		intron_variant		4
ENSG00000246090	ENST00000506454.1	n.166+16718C>A		intron_variant		3

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

Gnomad4 AFR AF: 0.283

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.777

Gnomad4 SAS AF: 0.442

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.254

Alfa AF: 0.233 Hom.: 3847

Bravo AF: 0.264

Asia WGS AF: 0.469 AC: 1626 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10008281; hg19: chr4-100142302;