chr5-80519838-A-T

Variant names:

• chr5-80519838-A-T
• rs904634864
• NM_205548.3:c.463A>T

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_205548.3(FAM151B):​c.463A>T​(p.Ile155Leu) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: FAM151B NM_205548.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 3.89
• Publications: 0 publications found

Genes affected

FAM151B (HGNC:33716): (family with sequence similarity 151 member B) Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_205548.3. 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
	FAM151B	NM_205548.3	MANE Select	c.463A>T	p.Ile155Leu	missense	Exon 4 of 6	NP_991111.2	Q6UXP7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM151B	ENST00000282226.5	TSL:1 MANE Select	c.463A>T	p.Ile155Leu	missense	Exon 4 of 6	ENSP00000282226.4	Q6UXP7
	FAM151B	ENST00000869019.1		c.337A>T	p.Ile113Leu	missense	Exon 3 of 5	ENSP00000539078.1
	FAM151B	ENST00000509292.1	TSL:3	n.425A>T		non_coding_transcript_exon	Exon 3 of 4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.078
BayesDel_addAF	Benign	-0.32	T
BayesDel_noAF	Benign	-0.69
CADD	Uncertain	23
DANN	Uncertain	0.98
DEOGEN2	Benign	0.0052	T
Eigen	Benign	-0.28
Eigen_PC	Benign	-0.030
FATHMM_MKL	Uncertain	0.92	D
LIST_S2	Benign	0.41	T
M_CAP	Benign	0.0041	T
MetaRNN	Benign	0.10	T
MetaSVM	Benign	-0.97	T
MutationAssessor	Benign	0.0	N
PhyloP100		3.9
PrimateAI	Benign	0.46	T
PROVEAN	Benign	0.40	N
REVEL	Benign	0.082
Sift	Benign	0.24	T
Sift4G	Benign	0.28	T
Polyphen		0.0	B
Vest4		0.11
MutPred		0.35		Loss of glycosylation at S156 (P = 0.2744)
MVP		0.030
MPC		0.10
ClinPred		0.45	T
GERP RS		5.8
Varity_R		0.15
gMVP		0.29
Mutation Taster		=97/3	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.28		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.28		Position offset: 16

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

Other links and lift over

dbSNP: rs904634864; hg19: chr5-79815657;