rs1122931

Positions:

• chr8-138416794-A-T

Variant summary

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

The NM_015912.4(FAM135B):​c.-19-48792T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,048 control chromosomes in the GnomAD database, including 1,641 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 0.13 (1641 hom., cov: 32)
• Consequence: FAM135B NM_015912.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.667

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.26 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM135B	NM_015912.4	c.-19-48792T>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.-19-48792T>A		intron_variant		5	NM_015912.4	ENSP00000378710	P1

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19233 AN: 151930 Hom.: 1630 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.0461

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0756

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.127 AC: 19271 AN: 152048 Hom.: 1641 Cov.: 32 AF XY: 0.131 AC XY: 9747 AN XY: 74310

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.267

Gnomad4 ASJ AF: 0.0461

Gnomad4 EAS AF: 0.257

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.0756

Gnomad4 OTH AF: 0.122

Alfa AF: 0.0994 Hom.: 117

Bravo AF: 0.139

Asia WGS AF: 0.209 AC: 727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.7
DANN	Benign	0.54

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: rs1122931; hg19: chr8-139429037;