rs3781452

Variant names:

• chr10-124666560-C-T
• rs3781452
• NM_014661.4:c.906+15047G>A

Variant summary

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

The NM_014661.4(FAM53B):​c.906+15047G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.595 in 151,990 control chromosomes in the GnomAD database, including 27,150 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 0.60 (27150 hom., cov: 33)
• Consequence: FAM53B NM_014661.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.560
• Publications: 14 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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.62 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM53B	NM_014661.4	c.906+15047G>A		intron_variant	Intron 4 of 4	ENST00000337318.8	NP_055476.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM53B	ENST00000337318.8	c.906+15047G>A		intron_variant	Intron 4 of 4	1	NM_014661.4	ENSP00000338532.3
ENSG00000258539	ENST00000494792.1	n.*1103+15047G>A		intron_variant	Intron 9 of 9	5		ENSP00000455755.1
FAM53B	ENST00000392754.7	c.906+15047G>A		intron_variant	Intron 4 of 4	2		ENSP00000376509.3

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90426 AN: 151870 Hom.: 27132 Cov.: 33

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.608

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

GnomAD4 genome AF: 0.595 AC: 90475 AN: 151990 Hom.: 27150 Cov.: 33 AF XY: 0.590 AC XY: 43822 AN XY: 74276

African (AFR) AF: 0.589 AC: 24392 AN: 41436

American (AMR) AF: 0.598 AC: 9145 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1685 AN: 3472

East Asian (EAS) AF: 0.545 AC: 2817 AN: 5166

South Asian (SAS) AF: 0.499 AC: 2408 AN: 4828

European-Finnish (FIN) AF: 0.526 AC: 5552 AN: 10546

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.625 AC: 42466 AN: 67944

Other (OTH) AF: 0.603 AC: 1269 AN: 2104

Alfa AF: 0.614 Hom.: 24341

Bravo AF: 0.600

Asia WGS AF: 0.487 AC: 1696 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.33
DANN	Benign	0.66
PhyloP100		-0.56
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: rs3781452; hg19: chr10-126355129; COSMIC: COSV55102326; COSMIC: COSV55102326;