NM_015912.4:c.158-21080G>A

Variant names:

• chr8-138286922-C-T
• rs1512406
• NM_015912.4:c.158-21080G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015912.4(FAM135B):​c.158-21080G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.628 in 152,100 control chromosomes in the GnomAD database, including 30,110 homozygotes. 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: 𝑓 0.63 (30110 hom., cov: 33)
• Consequence: FAM135B NM_015912.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.304
• Publications: 4 publications found

Genes affected

FAM135B (HGNC:28029): (family with sequence similarity 135 member B) Predicted to be involved in cellular lipid metabolic process. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015912.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM135B	NM_015912.4	MANE Select	c.158-21080G>A		intron	N/A	NP_056996.2
	FAM135B	NM_001362965.2		c.158-21080G>A		intron	N/A	NP_001349894.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM135B	ENST00000395297.6	TSL:5 MANE Select	c.158-21080G>A		intron	N/A	ENSP00000378710.1
	FAM135B	ENST00000482951.6	TSL:1	n.*104-21080G>A		intron	N/A	ENSP00000429874.1
	FAM135B	ENST00000160713.8	TSL:3	c.158-21080G>A		intron	N/A	ENSP00000160713.4

Frequencies

GnomAD3 genomes AF: 0.628 AC: 95483 AN: 151980 Hom.: 30089 Cov.: 33

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.725

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.628 AC: 95552 AN: 152100 Hom.: 30110 Cov.: 33 AF XY: 0.626 AC XY: 46499 AN XY: 74332

African (AFR) AF: 0.628 AC: 26045 AN: 41486

American (AMR) AF: 0.725 AC: 11084 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.611 AC: 2122 AN: 3472

East Asian (EAS) AF: 0.434 AC: 2242 AN: 5166

South Asian (SAS) AF: 0.566 AC: 2724 AN: 4816

European-Finnish (FIN) AF: 0.596 AC: 6301 AN: 10566

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.632 AC: 42970 AN: 67984

Other (OTH) AF: 0.623 AC: 1318 AN: 2114

Alfa AF: 0.624 Hom.: 34037

Bravo AF: 0.638

Asia WGS AF: 0.489 AC: 1703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.5
DANN	Benign	0.72
PhyloP100		0.30
Mutation Taster		=100/0	polymorphism (auto)

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: rs1512406; hg19: chr8-139299165;