rs759062810

Variant names:

• chr2-61825639-CTTTTTTT-C
• rs759062810
• NM_001201543.2:c.*809_*815delAAAAAAA

Your query was ambiguous. Multiple possible variants found:

• chr2-61825639-CTTTTTTT-C
• chr2-61825639-CTTTTTTT-CTTT
• chr2-61825639-CTTTTTTT-CTTTT
• chr2-61825639-CTTTTTTT-CTTTTT
• chr2-61825639-CTTTTTTT-CTTTTTT
• chr2-61825639-CTTTTTTT-CTTTTTTTT
• chr2-61825639-CTTTTTTT-CTTTTTTTTT
• chr2-61825639-CTTTTTTT-CTTTTTTTTTT
• chr2-61825639-CTTTTTTT-CTTTTTTTTTTT

Variant summary

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

The NM_001201543.2(FAM161A):​c.*809_*815delAAAAAAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000349 in 400,718 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000056 (0 hom., cov: 31)
  • Exomes 𝑓: 0.000023 (0 hom.)
• Consequence: FAM161A NM_001201543.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.42
• 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: Uncertain_significance. The variant received 0 ACMG points.

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.*809_*815delAAAAAAA		3_prime_UTR	Exon 7 of 7	NP_001188472.1	Q3B820-3
	FAM161A	NM_032180.3		c.*809_*815delAAAAAAA		3_prime_UTR	Exon 6 of 6	NP_115556.2	Q3B820-1
	FAM161A	NR_037710.2		n.2755_2761delAAAAAAA		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.*809_*815delAAAAAAA		3_prime_UTR	Exon 7 of 7	ENSP00000385158.1	Q3B820-3
	FAM161A	ENST00000405894.3	TSL:1	c.*809_*815delAAAAAAA		3_prime_UTR	Exon 6 of 6	ENSP00000385893.3	Q3B820-1
	FAM161A	ENST00000456262.5	TSL:1	n.*2307_*2313delAAAAAAA		non_coding_transcript_exon	Exon 6 of 6	ENSP00000396105.1	F8WCZ8

Frequencies

GnomAD3 genomes AF: 0.0000564 AC: 8 AN: 141818 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000943

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000232 AC: 6 AN: 258900 Hom.: 0 AF XY: 0.0000201 AC XY: 3 AN XY: 149068

African (AFR) AF: 0.00 AC: 0 AN: 5884

American (AMR) AF: 0.00 AC: 0 AN: 17024

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 8798

East Asian (EAS) AF: 0.00 AC: 0 AN: 8906

South Asian (SAS) AF: 0.00 AC: 0 AN: 50080

European-Finnish (FIN) AF: 0.000561 AC: 6 AN: 10686

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 880

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 144604

Other (OTH) AF: 0.00 AC: 0 AN: 12038

GnomAD4 genome AF: 0.0000564 AC: 8 AN: 141818 Hom.: 0 Cov.: 31 AF XY: 0.000102 AC XY: 7 AN XY: 68720

African (AFR) AF: 0.00 AC: 0 AN: 38952

American (AMR) AF: 0.00 AC: 0 AN: 14066

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3344

East Asian (EAS) AF: 0.00 AC: 0 AN: 4962

South Asian (SAS) AF: 0.00 AC: 0 AN: 4466

European-Finnish (FIN) AF: 0.000943 AC: 8 AN: 8486

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 64468

Other (OTH) AF: 0.00 AC: 0 AN: 1886

Alfa AF: 0.0000431 Hom.: 8

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs759062810; hg19: chr2-62052774;