rs886056214

Variant names:

• chr2-61825106-T-C
• rs886056214
• NM_001201543.2:c.*1349A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-61825106-T-C
• chr2-61825106-T-A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001201543.2(FAM161A):​c.*1349A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000333 in 300,498 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000033 (0 hom.)
• Consequence: FAM161A NM_001201543.2 3_prime_UTR
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -1.18
• Publications: 0 publications found

Genes affected

FAM161A (HGNC:25808): (FAM161 centrosomal protein A) This gene belongs to the FAM161 family. It is expressed mainly in the retina. Mouse studies suggested that this gene is involved in development of retinal progenitors during embryogenesis, and that its activity is restricted to mature photoreceptors after birth. Mutations in this gene cause autosomal recessive retinitis pigmentosa-28. Alternatively spliced transcript variants have been identified.[provided by RefSeq, Jan 2011]

FAM161A Gene-Disease associations (from GenCC):

• retinitis pigmentosa 28

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
• retinitis pigmentosa

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001201543.2. 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
	FAM161A	NM_001201543.2	MANE Select	c.*1349A>G		3_prime_UTR	Exon 7 of 7	NP_001188472.1	Q3B820-3
	FAM161A	NM_032180.3		c.*1349A>G		3_prime_UTR	Exon 6 of 6	NP_115556.2	Q3B820-1
	FAM161A	NR_037710.2		n.3295A>G		non_coding_transcript_exon	Exon 6 of 6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM161A	ENST00000404929.6	TSL:1 MANE Select	c.*1349A>G		3_prime_UTR	Exon 7 of 7	ENSP00000385158.1	Q3B820-3
	FAM161A	ENST00000405894.3	TSL:1	c.*1349A>G		3_prime_UTR	Exon 6 of 6	ENSP00000385893.3	Q3B820-1
	FAM161A	ENST00000456262.5	TSL:1	n.*2847A>G		non_coding_transcript_exon	Exon 6 of 6	ENSP00000396105.1	F8WCZ8

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000333 AC: 1 AN: 300498 Hom.: 0 Cov.: 0 AF XY: 0.00000584 AC XY: 1 AN XY: 171188

African (AFR) AF: 0.00 AC: 0 AN: 8510

American (AMR) AF: 0.00 AC: 0 AN: 27110

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 10756

East Asian (EAS) AF: 0.00 AC: 0 AN: 9344

South Asian (SAS) AF: 0.00 AC: 0 AN: 58868

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 12340

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1140

European-Non Finnish (NFE) AF: 0.00000631 AC: 1 AN: 158446

Other (OTH) AF: 0.00 AC: 0 AN: 13984

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	Retinitis pigmentosa (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.10
DANN	Benign	0.76
PhyloP100		-1.2

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: rs886056214; hg19: chr2-62052241;