rs10794178

Variant names:

• chr10-124723355-G-A
• rs10794178
• NM_014661.4:c.-174-16468C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014661.4(FAM53B):​c.-174-16468C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 152,162 control chromosomes in the GnomAD database, including 8,783 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 0.33 (8783 hom., cov: 33)
• Consequence: FAM53B NM_014661.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.304
• Publications: 7 publications found

Genes affected

FAM53B (HGNC:28968): (family with sequence similarity 53 member B) Involved in positive regulation of canonical Wnt signaling pathway. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000258539 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM53B	NM_014661.4	c.-174-16468C>T		intron_variant	Intron 1 of 4	ENST00000337318.8	NP_055476.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM53B	ENST00000337318.8	c.-174-16468C>T		intron_variant	Intron 1 of 4	1	NM_014661.4	ENSP00000338532.3
FAM53B	ENST00000280780.6	c.-174-16468C>T		intron_variant	Intron 1 of 4	1		ENSP00000280780.6
ENSG00000258539	ENST00000494792.1	n.*24-16468C>T		intron_variant	Intron 6 of 9	5		ENSP00000455755.1
FAM53B	ENST00000392754.7	c.-174-16468C>T		intron_variant	Intron 1 of 4	2		ENSP00000376509.3

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50804 AN: 152044 Hom.: 8777 Cov.: 33

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.334 AC: 50828 AN: 152162 Hom.: 8783 Cov.: 33 AF XY: 0.329 AC XY: 24469 AN XY: 74414

African (AFR) AF: 0.291 AC: 12069 AN: 41512

American (AMR) AF: 0.414 AC: 6326 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1205 AN: 3470

East Asian (EAS) AF: 0.316 AC: 1635 AN: 5170

South Asian (SAS) AF: 0.320 AC: 1546 AN: 4830

European-Finnish (FIN) AF: 0.222 AC: 2350 AN: 10588

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.364 AC: 24745 AN: 67994

Other (OTH) AF: 0.357 AC: 752 AN: 2108

Alfa AF: 0.358 Hom.: 42630

Bravo AF: 0.345

Asia WGS AF: 0.298 AC: 1036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.3
DANN	Benign	0.75
PhyloP100		0.30
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10794178; hg19: chr10-126411924;