7-192800-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_020223.4(FAM20C):c.-400G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 147,466 control chromosomes in the GnomAD database, including 1,527 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.13 (1527 hom., cov: 31)
• Consequence: FAM20C NM_020223.4 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.45

Genes affected

FAM20C (HGNC:22140): (FAM20C golgi associated secretory pathway kinase) This gene encodes a member of the family of secreted protein kinases. The encoded protein binds calcium and phosphorylates proteins involved in bone mineralization. Mutations in this gene are associated with the autosomal recessive disorder Raine syndrome. [provided by RefSeq, Apr 2014]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BP6: Variant 7-192800-G-A is Benign according to our data. Variant chr7-192800-G-A is described in ClinVar as [Benign]. Clinvar id is 1270004.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM20C	NM_020223.4	c.-400G>A		5_prime_UTR_variant	1/10	ENST00000313766.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM20C	ENST00000313766.6	c.-400G>A		5_prime_UTR_variant	1/10	1	NM_020223.4	P1
	ENST00000467050.1	n.233+1148C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.135 AC: 19879 AN: 147362 Hom.: 1517 Cov.: 31

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.0567

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.135 AC: 19901 AN: 147466 Hom.: 1527 Cov.: 31 AF XY: 0.136 AC XY: 9774 AN XY: 71816

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.314

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.0567

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.166

Alfa AF: 0.113 Hom.: 126

Bravo AF: 0.136

Asia WGS AF: 0.286 AC: 838 AN: 2940

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Apr 27, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	11
Dann	Benign	0.90

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4577908; hg19: chr7-192800;