rs340708

chr8-138369303-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015912.4(FAM135B):c.-19-1301C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.486 in 151,878 control chromosomes in the GnomAD database, including 20,255 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 0.49 (20255 hom., cov: 31)
• Consequence: FAM135B NM_015912.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.378

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM135B	NM_015912.4	c.-19-1301C>A		intron_variant		ENST00000395297.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM135B	ENST00000395297.6	c.-19-1301C>A		intron_variant		5	NM_015912.4	P1

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73868 AN: 151760 Hom.: 20256 Cov.: 31

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.486 AC: 73874 AN: 151878 Hom.: 20255 Cov.: 31 AF XY: 0.484 AC XY: 35937 AN XY: 74186

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.429

Gnomad4 ASJ AF: 0.558

Gnomad4 EAS AF: 0.180

Gnomad4 SAS AF: 0.396

Gnomad4 FIN AF: 0.646

Gnomad4 NFE AF: 0.634

Gnomad4 OTH AF: 0.502

Alfa AF: 0.600 Hom.: 54982

Bravo AF: 0.463

Asia WGS AF: 0.285 AC: 993 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.58
Dann	Benign	0.55

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

Publications

LitVar

Other links and lift over

dbSNP: rs340708; hg19: chr8-139381546;