rs6425513

Positions:

• chr1-179037327-G-A

Variant summary

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

The NM_014864.4(FAM20B):​c.-133-6388G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.711 in 151,788 control chromosomes in the GnomAD database, including 39,493 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 0.71 (39493 hom., cov: 29)
• Consequence: FAM20B NM_014864.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

Genes affected

FAM20B (HGNC:23017): (FAM20B glycosaminoglycan xylosylkinase) Enables phosphotransferase activity, alcohol group as acceptor. Predicted to be involved in proteoglycan biosynthetic process. Located in Golgi apparatus and nucleoplasm. [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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM20B	NM_014864.4	c.-133-6388G>A		intron_variant		ENST00000263733.5	NP_055679.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM20B	ENST00000263733.5	c.-133-6388G>A		intron_variant		1	NM_014864.4	ENSP00000263733.4
FAM20B	ENST00000440702.5	c.-133-6388G>A		intron_variant		3		ENSP00000404005.1

Frequencies

GnomAD3 genomes AF: 0.711 AC: 107770 AN: 151672 Hom.: 39444 Cov.: 29

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.754

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.643

Gnomad OTH AF: 0.704

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

GnomAD4 genome AF: 0.711 AC: 107877 AN: 151788 Hom.: 39493 Cov.: 29 AF XY: 0.711 AC XY: 52717 AN XY: 74140

Gnomad4 AFR AF: 0.886

Gnomad4 AMR AF: 0.592

Gnomad4 ASJ AF: 0.693

Gnomad4 EAS AF: 0.595

Gnomad4 SAS AF: 0.604

Gnomad4 FIN AF: 0.754

Gnomad4 NFE AF: 0.643

Gnomad4 OTH AF: 0.708

Alfa AF: 0.647 Hom.: 50955

Bravo AF: 0.707

Asia WGS AF: 0.676 AC: 2352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.11
DANN	Benign	0.51

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: rs6425513; hg19: chr1-179006462;