rs954229404

Variant names:

• chr9-133579044-C-A
• rs954229404
• NM_001080515.3:c.479G>T

Your query was ambiguous. Multiple possible variants found:

• chr9-133579044-C-A
• chr9-133579044-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_001080515.3(FAM163B):​c.479G>T​(p.Arg160Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000142 in 1,408,842 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R160H) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: FAM163B NM_001080515.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.90

Genes affected

FAM163B (HGNC:33277): (family with sequence similarity 163 member B) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.3398769).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM163B	NM_001080515.3	c.479G>T	p.Arg160Leu	missense_variant	Exon 3 of 3	ENST00000673969.1	NP_001073984.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM163B	ENST00000673969.1	c.479G>T	p.Arg160Leu	missense_variant	Exon 3 of 3		NM_001080515.3	ENSP00000501259.1
FAM163B	ENST00000496132.2	c.479G>T	p.Arg160Leu	missense_variant	Exon 3 of 3	3		ENSP00000419867.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD3 exomes AF: 0.0000263 AC: 2 AN: 75932 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 40466

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000770

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000356

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000142 AC: 2 AN: 1408842 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 696424

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000264

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.0000172

GnomAD4 genome Cov.: 33

Bravo AF: 0.0000189

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.62
BayesDel_addAF	Uncertain	0.12	D
BayesDel_noAF	Uncertain	-0.060
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Benign	0.22	T;T
Eigen	Uncertain	0.40
Eigen_PC	Uncertain	0.37
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.91	D;.
M_CAP	Benign	0.068	D
MetaRNN	Benign	0.34	T;T
MetaSVM	Benign	-0.43	T
MutationAssessor	Uncertain	2.9	M;M
PrimateAI	Benign	0.47	T
PROVEAN	Pathogenic	-4.7	D;D
REVEL	Benign	0.16
Sift	Uncertain	0.010	D;D
Sift4G	Uncertain	0.017	D;D
Polyphen		0.96	D;D
Vest4		0.54
MutPred		0.36		Loss of MoRF binding (P = 6e-04);Loss of MoRF binding (P = 6e-04);
MVP		0.095
MPC		2.2
ClinPred		0.85	D
GERP RS		4.1
Varity_R		0.27
gMVP		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: rs954229404; hg19: chr9-136444166;