ENST00000455905.1:n.137-11005G>T

Variant names:

• chr7-99549571-A-T
• NM_145111.4:c.-99-1065T>A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_145111.4(FAM200A):​c.-99-1065T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: FAM200A NM_145111.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131

Genes affected

FAM200A (HGNC:25401): (family with sequence similarity 200 member A) This gene encodes a protein of unknown function. The protein is weakly similar to transposase-like proteins in human and mouse. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM200A	NM_145111.4	c.-99-1065T>A		intron_variant	Intron 1 of 1	ENST00000449309.2	NP_659802.1
FAM200A	XM_024446681.2	c.-99-1065T>A		intron_variant	Intron 1 of 1		XP_024302449.1
FAM200A	XM_047420022.1	c.-99-1065T>A		intron_variant	Intron 2 of 2		XP_047275978.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM200A	ENST00000449309.2	c.-99-1065T>A		intron_variant	Intron 1 of 1	1	NM_145111.4	ENSP00000411372.1
FAM200A	ENST00000408938.2	c.-99-1065T>A		intron_variant	Intron 1 of 1	2		ENSP00000386191.2

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.8
DANN	Benign	0.86

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr7-99147194;