chr8-12551601-A-T

Variant names:

• chr8-12551601-A-T
• rs2452658
• ENST00000635775.1:n.1973-12536T>A

Variant summary

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

The ENST00000635775.1(ENSG00000283674):​n.1973-12536T>A 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: 83)
• Consequence: ENSG00000283674 ENST00000635775.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0690
• Publications: 1 publications found

Genes affected

ENSG00000283674 (HGNC:):

FAM66A (HGNC:30444): (family with sequence similarity 66 member A)

FAM86B2-DT (HGNC:48726): (FAM86B2 divergent transcript)

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=-0.91).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000635775.1. 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
	FAM86B2-DT	NR_040092.1		n.1337-14285A>T		intron	N/A
	LOC729732	NR_047662.2		n.1996-12536T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000283674	ENST00000635775.1	TSL:2	n.1973-12536T>A		intron	N/A
	ENSG00000283674	ENST00000641618.1		n.587+29227T>A		intron	N/A
	ENSG00000283674	ENST00000641839.1		n.684-40344T>A		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 83

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

GnomAD4 genome Cov.: 83

Alfa AF: 0.00 Hom.: 232

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.8
DANN	Benign	0.68
PhyloP100		-0.069

Splicing

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

Other links and lift over

dbSNP: rs2452658; hg19: chr8-12409110;