chrX-55157818-A-T

Position:

• chrX-55157818-A-T

Variant summary

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

The NM_001166701.4(FAM104B):​c.120+1311T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 110,313 control chromosomes in the GnomAD database, including 9,346 homozygotes. There are 15,690 hemizygotes in GnomAD. 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 0.48 (9346 hom., 15690 hem., cov: 22)
• Consequence: FAM104B NM_001166701.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.582

Genes affected

FAM104B (HGNC:25085): (VCP nuclear cofactor family member 2)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM104B	NM_001166701.4	c.120+1311T>A		intron_variant		ENST00000685693.1	NP_001160173.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM104B	ENST00000685693.1	c.120+1311T>A		intron_variant			NM_001166701.4	ENSP00000509111	A2

Frequencies

GnomAD3 genomes AF: 0.478 AC: 52760 AN: 110266 Hom.: 9352 Cov.: 22 AF XY: 0.481 AC XY: 15656 AN XY: 32560

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.478 AC: 52775 AN: 110313 Hom.: 9346 Cov.: 22 AF XY: 0.481 AC XY: 15690 AN XY: 32619

Gnomad4 AFR AF: 0.336

Gnomad4 AMR AF: 0.446

Gnomad4 ASJ AF: 0.452

Gnomad4 EAS AF: 0.526

Gnomad4 SAS AF: 0.538

Gnomad4 FIN AF: 0.600

Gnomad4 NFE AF: 0.552

Gnomad4 OTH AF: 0.404

Alfa AF: 0.527 Hom.: 3848

Bravo AF: 0.460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.64
DANN	Benign	0.73

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: rs1874111; hg19: chrX-55184251;