2-61825639-CT-C

Position:

• chr2-61825639-CT-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001201543.2(FAM161A):​c.*815del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 354,656 control chromosomes in the GnomAD database, including 9 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.0072 (9 hom., cov: 31)
  • Exomes 𝑓: 0.17 (0 hom.)
• Consequence: FAM161A NM_001201543.2 3_prime_UTR
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• 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 Benign. Variant got -8 ACMG points.

• BA1: GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM161A	NM_001201543.2	c.*815del		3_prime_UTR_variant	7/7	ENST00000404929.6	NP_001188472.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM161A	ENST00000404929.6	c.*815del		3_prime_UTR_variant	7/7	1	NM_001201543.2	ENSP00000385158	P1
FAM161A	ENST00000405894.3	c.*815del		3_prime_UTR_variant	6/6	1		ENSP00000385893
FAM161A	ENST00000456262.5	c.*2313del		3_prime_UTR_variant, NMD_transcript_variant	6/6	1		ENSP00000396105
FAM161A	ENST00000418113.5	c.*1438del		3_prime_UTR_variant, NMD_transcript_variant	8/8	5		ENSP00000416861

Frequencies

GnomAD3 genomes AF: 0.00719 AC: 1019 AN: 141724 Hom.: 9 Cov.: 31

Gnomad AFR AF: 0.0188

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00320

Gnomad ASJ AF: 0.00568

Gnomad EAS AF: 0.00242

Gnomad SAS AF: 0.000896

Gnomad FIN AF: 0.00863

Gnomad MID AF: 0.00342

Gnomad NFE AF: 0.00189

Gnomad OTH AF: 0.00583

GnomAD4 exome AF: 0.175 AC: 37206 AN: 212944 Hom.: 0 Cov.: 0 AF XY: 0.173 AC XY: 21252 AN XY: 122766

Gnomad4 AFR exome AF: 0.188

Gnomad4 AMR exome AF: 0.184

Gnomad4 ASJ exome AF: 0.184

Gnomad4 EAS exome AF: 0.176

Gnomad4 SAS exome AF: 0.171

Gnomad4 FIN exome AF: 0.174

Gnomad4 NFE exome AF: 0.174

Gnomad4 OTH exome AF: 0.178

GnomAD4 genome AF: 0.00720 AC: 1020 AN: 141712 Hom.: 9 Cov.: 31 AF XY: 0.00779 AC XY: 535 AN XY: 68670

Gnomad4 AFR AF: 0.0188

Gnomad4 AMR AF: 0.00320

Gnomad4 ASJ AF: 0.00568

Gnomad4 EAS AF: 0.00243

Gnomad4 SAS AF: 0.000900

Gnomad4 FIN AF: 0.00863

Gnomad4 NFE AF: 0.00189

Gnomad4 OTH AF: 0.00582

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Retinitis Pigmentosa, Recessive Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

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;