chr1-206199880-C-T

Variant names:

• chr1-206199880-C-T
• NM_001123168.3:c.157G>A

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001123168.3(FAM72A):​c.157G>A​(p.Val53Met) variant causes a missense change. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 19)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: FAM72A NM_001123168.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 4.73
• Publications: 0 publications found

Genes affected

FAM72A (HGNC:24044): (family with sequence similarity 72 member A) Predicted to act upstream of or within negative regulation of brain-derived neurotrophic factor-activated receptor activity and positive regulation of apoptotic process. Located in cytosol and intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001123168.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM72A	NM_001123168.3	MANE Select	c.157G>A	p.Val53Met	missense	Exon 2 of 4	NP_001116640.1	Q5TYM5-1
	FAM72A	NM_001317901.2		c.157G>A	p.Val53Met	missense	Exon 2 of 4	NP_001304830.1	Q5TYM6
	FAM72A	NM_001385240.1		c.157G>A	p.Val53Met	missense	Exon 4 of 6	NP_001372169.1	Q5TYM5-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM72A	ENST00000367128.8	TSL:1 MANE Select	c.157G>A	p.Val53Met	missense	Exon 2 of 4	ENSP00000356096.3	Q5TYM5-1
	FAM72A	ENST00000341209.9	TSL:1	c.37G>A	p.Val13Met	missense	Exon 2 of 4	ENSP00000340661.5	Q5TYM5-2
	FAM72A	ENST00000367129.6	TSL:3	c.157G>A	p.Val53Met	missense	Exon 2 of 4	ENSP00000356097.2	Q5TYM6

Frequencies

GnomAD3 genomes Cov.: 19

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 558958 Hom.: 0 Cov.: 5 AF XY: 0.00 AC XY: 0 AN XY: 302652

African (AFR) AF: 0.00 AC: 0 AN: 15244

American (AMR) AF: 0.00 AC: 0 AN: 30758

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 17090

East Asian (EAS) AF: 0.00 AC: 0 AN: 34708

South Asian (SAS) AF: 0.00 AC: 0 AN: 58352

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 49918

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2204

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 320750

Other (OTH) AF: 0.00 AC: 0 AN: 29934

GnomAD4 genome Cov.: 19

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.71
BayesDel_noAF	Pathogenic	0.15
CADD	Pathogenic	26
DANN	Uncertain	1.0
DEOGEN2	Benign	0.025	T
LIST_S2	Uncertain	0.91	D
MetaRNN	Uncertain	0.58	D
PhyloP100		4.7
PROVEAN	Benign	-1.6	N
Sift	Uncertain	0.0070	D
Sift4G	Uncertain	0.0040	D
Vest4		0.48
gMVP		0.50

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

hg19: chr1-206141450;