2-61825639-CTTTTTTT-CTTTTT

Variant names:

• chr2-61825639-CTT-C
• rs759062810
• NM_001201543.2:c.*814_*815delAA

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BS1

The NM_001201543.2(FAM161A):​c.*814_*815delAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0124 in 376,962 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 0.00026 (0 hom., cov: 31)
  • Exomes 𝑓: 0.020 (0 hom.)
• Consequence: FAM161A NM_001201543.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.432

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]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BS1: Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.0198 (4647/235274) while in subpopulation MID AF= 0.0305 (24/786). AF 95% confidence interval is 0.0269. There are 0 homozygotes in gnomad4_exome. There are 2679 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM161A	NM_001201543.2	c.*814_*815delAA		3_prime_UTR_variant	Exon 7 of 7	ENST00000404929.6	NP_001188472.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM161A	ENST00000404929	c.*814_*815delAA		3_prime_UTR_variant	Exon 7 of 7	1	NM_001201543.2	ENSP00000385158.1

Frequencies

GnomAD3 genomes AF: 0.000261 AC: 37 AN: 141702 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.000154

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.000299

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00189

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000202

Gnomad OTH AF: 0.000530

GnomAD4 exome AF: 0.0198 AC: 4647 AN: 235274 Hom.: 0 AF XY: 0.0197 AC XY: 2679 AN XY: 135768

Gnomad4 AFR exome AF: 0.0241

Gnomad4 AMR exome AF: 0.0291

Gnomad4 ASJ exome AF: 0.0306

Gnomad4 EAS exome AF: 0.0168

Gnomad4 SAS exome AF: 0.0197

Gnomad4 FIN exome AF: 0.0183

Gnomad4 NFE exome AF: 0.0181

Gnomad4 OTH exome AF: 0.0193

GnomAD4 genome AF: 0.000261 AC: 37 AN: 141688 Hom.: 0 Cov.: 31 AF XY: 0.000335 AC XY: 23 AN XY: 68662

Gnomad4 AFR AF: 0.000154

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.000299

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00189

Gnomad4 NFE AF: 0.000202

Gnomad4 OTH AF: 0.000529

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

LitVar

Other links and lift over

dbSNP: rs759062810; hg19: chr2-62052774;