8-138291592-T-C

Variant names:

• chr8-138291592-T-C
• rs1512407
• NM_015912.4:c.157+19249A>G

Variant summary

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

The NM_015912.4(FAM135B):​c.157+19249A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.939 in 152,242 control chromosomes in the GnomAD database, including 67,376 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 0.94 (67376 hom., cov: 32)
• Consequence: FAM135B NM_015912.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.390

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=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.984 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM135B	NM_015912.4	c.157+19249A>G		intron_variant	Intron 3 of 19	ENST00000395297.6	NP_056996.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM135B	ENST00000395297.6	c.157+19249A>G		intron_variant	Intron 3 of 19	5	NM_015912.4	ENSP00000378710.1

Frequencies

GnomAD3 genomes AF: 0.939 AC: 142793 AN: 152124 Hom.: 67336 Cov.: 32

Gnomad AFR AF: 0.858

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.917

Gnomad ASJ AF: 0.955

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.948

Gnomad FIN AF: 0.993

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.990

Gnomad OTH AF: 0.945

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

GnomAD4 genome AF: 0.939 AC: 142888 AN: 152242 Hom.: 67376 Cov.: 32 AF XY: 0.939 AC XY: 69899 AN XY: 74438

Gnomad4 AFR AF: 0.858

Gnomad4 AMR AF: 0.917

Gnomad4 ASJ AF: 0.955

Gnomad4 EAS AF: 0.819

Gnomad4 SAS AF: 0.948

Gnomad4 FIN AF: 0.993

Gnomad4 NFE AF: 0.990

Gnomad4 OTH AF: 0.945

Alfa AF: 0.955 Hom.: 5601

Bravo AF: 0.929

Asia WGS AF: 0.883 AC: 3065 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.31
DANN	Benign	0.60

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: rs1512407; hg19: chr8-139303835;