chr5-80498283-A-T

Variant names:

• chr5-80498283-A-T
• rs248999
• NM_205548.3:c.26-3509A>T

Variant summary

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

The NM_205548.3(FAM151B):​c.26-3509A>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: 30)
• Consequence: FAM151B NM_205548.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490
• Publications: 2 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: 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=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM151B	NM_205548.3	c.26-3509A>T		intron_variant	Intron 1 of 5	ENST00000282226.5	NP_991111.2
FAM151B	XM_011543234.3	c.73+3000A>T		intron_variant	Intron 1 of 5		XP_011541536.1
FAM151B	XM_011543235.3	c.25+10135A>T		intron_variant	Intron 1 of 4		XP_011541537.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM151B	ENST00000282226.5	c.26-3509A>T		intron_variant	Intron 1 of 5	1	NM_205548.3	ENSP00000282226.4
FAM151B	ENST00000502608.5	n.26-3509A>T		intron_variant	Intron 1 of 3	3		ENSP00000427035.1
FAM151B	ENST00000507084.1	n.257-1602A>T		intron_variant	Intron 2 of 4	3
FAM151B	ENST00000511718.5	n.395-1602A>T		intron_variant	Intron 2 of 10	2

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.7
DANN	Benign	0.74
PhyloP100		-0.049

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs248999; hg19: chr5-79794102;