ENST00000522601.5:n.904+3282A>T

Variant names:

• chr8-8240557-A-T
• rs2955587
• ENST00000522601.5:n.904+3282A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000522601.5(FAM86B3P):​n.904+3282A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: FAM86B3P ENST00000522601.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370
• Publications: 12 publications found

Genes affected

FAM86B3P (HGNC:):

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

FAM85B (HGNC:32160): (family with sequence similarity 85 member B)

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

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALG1L13P		n.8240557A>T		intragenic_variant
FAM86B3P	NR_024361.1	n.929+3282A>T		intron_variant	Intron 7 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM86B3P	ENST00000522601.5	n.904+3282A>T		intron_variant	Intron 7 of 8	1
FAM86B3P	ENST00000310542.3	n.189A>T		non_coding_transcript_exon_variant	Exon 1 of 2	2
ALG1L13P	ENST00000519320.1	n.117-9T>A		intron_variant	Intron 1 of 4	6

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 1437982 Hom.: 0 Cov.: 41 AF XY: 0.00 AC XY: 0 AN XY: 715456

African (AFR) AF: 0.00 AC: 0 AN: 32988

American (AMR) AF: 0.00 AC: 0 AN: 43878

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25626

East Asian (EAS) AF: 0.00 AC: 0 AN: 39278

South Asian (SAS) AF: 0.00 AC: 0 AN: 85668

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 51814

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4528

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1095136

Other (OTH) AF: 0.00 AC: 0 AN: 59066

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.75
DANN	Benign	0.81
PhyloP100		-0.037

Splicing

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

Other links and lift over

dbSNP: rs2955587; hg19: chr8-8098079;