8-8237303-T-G

Variant names:

• chr8-8237303-T-G
• rs2980438
• ENST00000522601.5:n.904+28T>G

Variant summary

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

The ENST00000834326.1(FAM85B):​n.891A>C variant causes a non coding transcript exon 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)
• Consequence: FAM85B ENST00000834326.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 9 publications found

Genes affected

FAM86B3P (HGNC:):

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

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

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=-0.88).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000834326.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM86B3P	NR_024361.1		n.929+28T>G		intron	N/A
	FAM86B3P	NR_024362.1		n.1026+28T>G		intron	N/A
	FAM86B3P	NR_024363.1		n.656+28T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM86B3P	ENST00000522601.5	TSL:1	n.904+28T>G		intron	N/A
	FAM86B3P	ENST00000588728.5	TSL:1	n.626+28T>G		intron	N/A
	FAM85B	ENST00000834326.1		n.891A>C		non_coding_transcript_exon	Exon 7 of 7

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 14

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.39
PhyloP100		-1.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Other links and lift over

dbSNP: rs2980438; hg19: chr8-8094825;