8-138286922-C-T

Position:

• chr8-138286922-C-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM135B	NM_015912.4	c.158-21080G>A		intron_variant		ENST00000395297.6	NP_056996.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM135B	ENST00000395297.6	c.158-21080G>A		intron_variant		5	NM_015912.4	ENSP00000378710	P1

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

Gnomad4 AFR AF: 0.628

Gnomad4 AMR AF: 0.725

Gnomad4 ASJ AF: 0.611

Gnomad4 EAS AF: 0.434

Gnomad4 SAS AF: 0.566

Gnomad4 FIN AF: 0.596

Gnomad4 NFE AF: 0.632

Gnomad4 OTH AF: 0.623

Alfa AF: 0.621 Hom.: 29459

Bravo AF: 0.638

Asia WGS AF: 0.489 AC: 1703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.5
DANN	Benign	0.72

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: rs1512406; hg19: chr8-139299165;