rs1297676726

Variant names:

• chr1-206199826-C-T
• rs1297676726
• NM_001123168.3:c.211G>A

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP4

The NM_001123168.3(FAM72A):​c.211G>A​(p.Asp71Asn) variant causes a missense change. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 10)
  • Exomes 𝑓: 0.0000049 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: FAM72A NM_001123168.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 3.76
• 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: Likely_benign. The variant received -1 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.26816624).

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.211G>A	p.Asp71Asn	missense	Exon 2 of 4	NP_001116640.1	Q5TYM5-1
	FAM72A	NM_001317901.2		c.211G>A	p.Asp71Asn	missense	Exon 2 of 4	NP_001304830.1	Q5TYM6
	FAM72A	NM_001385240.1		c.211G>A	p.Asp71Asn	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.211G>A	p.Asp71Asn	missense	Exon 2 of 4	ENSP00000356096.3	Q5TYM5-1
	FAM72A	ENST00000341209.9	TSL:1	c.91G>A	p.Asp31Asn	missense	Exon 2 of 4	ENSP00000340661.5	Q5TYM5-2
	FAM72A	ENST00000367129.6	TSL:3	c.211G>A	p.Asp71Asn	missense	Exon 2 of 4	ENSP00000356097.2	Q5TYM6

Frequencies

GnomAD3 genomes Cov.: 10

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000487 AC: 3 AN: 616288 Hom.: 0 Cov.: 8 AF XY: 0.00 AC XY: 0 AN XY: 330460

African (AFR) AF: 0.00 AC: 0 AN: 17180

American (AMR) AF: 0.0000773 AC: 3 AN: 38800

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18468

East Asian (EAS) AF: 0.00 AC: 0 AN: 34912

South Asian (SAS) AF: 0.00 AC: 0 AN: 62236

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 50412

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2342

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 359806

Other (OTH) AF: 0.00 AC: 0 AN: 32132

GnomAD4 genome Cov.: 10

Alfa AF: 0.00 Hom.: 0

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	Benign	0.32
BayesDel_noAF	Pathogenic	0.31
CADD	Benign	21
DANN	Uncertain	0.99
DEOGEN2	Benign	0.054	T
LIST_S2	Uncertain	0.89	D
MetaRNN	Benign	0.27	T
PhyloP100		3.8
PROVEAN	Uncertain	-2.4	N
Sift	Benign	0.16	T
Sift4G	Benign	0.25	T
Vest4		0.27
gMVP		0.52

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

dbSNP: rs1297676726; hg19: chr1-206141504;