ENST00000522601.5:n.904+28T>A

Variant names:

• chr8-8237303-T-A
• ENST00000522601.5:n.904+28T>A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000522601.5(FAM86B3P):​n.904+28T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000102 in 976,326 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0000010 (0 hom.)
• Consequence: FAM86B3P ENST00000522601.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

Genes affected

FAM86B3P (HGNC:):

ALG1L13P (HGNC:44382): (ALG1 like 13, pseudogene)

FAM86B3P (HGNC:44371): (family with sequence similarity 86 member B3, pseudogene)

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALG1L13P		n.8237303T>A		intragenic_variant
FAM86B3P	NR_024361.1	n.929+28T>A		intron_variant	Intron 7 of 8
FAM86B3P	NR_024362.1	n.1026+28T>A		intron_variant	Intron 7 of 7
FAM86B3P	NR_024363.1	n.656+28T>A		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM86B3P	ENST00000522601.5	n.904+28T>A		intron_variant	Intron 7 of 8	1
FAM86B3P	ENST00000588728.5	n.626+28T>A		intron_variant	Intron 5 of 5	1
ENSG00000291048	ENST00000518201.1	n.160+888A>T		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000102 AC: 1 AN: 976326 Hom.: 0 Cov.: 14 AF XY: 0.00000198 AC XY: 1 AN XY: 505588

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000145

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.91
DANN	Benign	0.53

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr8-8094825;