NM_015912.4:c.158-13645G>A

Variant names:

• chr8-138279487-C-T
• rs1398296
• NM_015912.4:c.158-13645G>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.158-13645G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 152,096 control chromosomes in the GnomAD database, including 9,339 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 0.34 (9339 hom., cov: 33)
• Consequence: FAM135B NM_015912.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83
• Publications: 2 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=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.408 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.158-13645G>A		intron	N/A	NP_056996.2
	FAM135B	NM_001362965.2		c.158-13645G>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.158-13645G>A		intron	N/A	ENSP00000378710.1
	FAM135B	ENST00000482951.6	TSL:1	n.*104-13645G>A		intron	N/A	ENSP00000429874.1
	FAM135B	ENST00000160713.8	TSL:3	c.158-13645G>A		intron	N/A	ENSP00000160713.4

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52249 AN: 151978 Hom.: 9335 Cov.: 33

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.344 AC: 52267 AN: 152096 Hom.: 9339 Cov.: 33 AF XY: 0.344 AC XY: 25573 AN XY: 74356

African (AFR) AF: 0.413 AC: 17115 AN: 41470

American (AMR) AF: 0.392 AC: 5996 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1056 AN: 3464

East Asian (EAS) AF: 0.218 AC: 1126 AN: 5176

South Asian (SAS) AF: 0.418 AC: 2013 AN: 4820

European-Finnish (FIN) AF: 0.301 AC: 3180 AN: 10582

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.307 AC: 20865 AN: 67974

Other (OTH) AF: 0.307 AC: 649 AN: 2114

Alfa AF: 0.319 Hom.: 16111

Bravo AF: 0.349

Asia WGS AF: 0.289 AC: 1009 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.17
PhyloP100		-1.8
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: rs1398296; hg19: chr8-139291730;