2-61825639-CTTTTTTT-CTTTTTTTTT

Variant names:

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

Variant summary

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

The NM_001201543.2(FAM161A):​c.*814_*815dupAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00125 in 397,562 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 0.000028 (0 hom., cov: 31)
  • Exomes 𝑓: 0.0019 (0 hom.)
• Consequence: FAM161A NM_001201543.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.158

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 amr. gnomad4_exome allele frequency = 0.00193 (493/255760) while in subpopulation AMR AF= 0.00297 (50/16832). AF 95% confidence interval is 0.00231. There are 0 homozygotes in gnomad4_exome. There are 300 alleles in male gnomad4_exome subpopulation. Median coverage is 0. This position pass quality control queck.

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes AF: 0.0000282 AC: 4 AN: 141814 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000711

Gnomad ASJ AF: 0.000299

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000236

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00193 AC: 493 AN: 255760 Hom.: 0 Cov.: 0 AF XY: 0.00204 AC XY: 300 AN XY: 147264

Gnomad4 AFR exome AF: 0.00223

Gnomad4 AMR exome AF: 0.00297

Gnomad4 ASJ exome AF: 0.00207

Gnomad4 EAS exome AF: 0.00273

Gnomad4 SAS exome AF: 0.00218

Gnomad4 FIN exome AF: 0.000758

Gnomad4 NFE exome AF: 0.00171

Gnomad4 OTH exome AF: 0.00227

GnomAD4 genome AF: 0.0000282 AC: 4 AN: 141802 Hom.: 0 Cov.: 31 AF XY: 0.0000291 AC XY: 2 AN XY: 68730

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.0000710

Gnomad4 ASJ AF: 0.000299

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000236

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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;