chr22-27922204-G-C

Position:

• chr22-27922204-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_026963.1(TTC28-AS1):​n.170+2659G>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0969 in 152,252 control chromosomes in the GnomAD database, including 801 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.097 (801 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: TTC28-AS1 NR_026963.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.160

Genes affected

TTC28-AS1 (HGNC:29336): (TTC28 antisense RNA 1)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TTC28-AS1	NR_026963.1	n.170+2659G>C		intron_variant, non_coding_transcript_variant
TTC28-AS1	NR_026962.1	n.331+26G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TTC28-AS1	ENST00000454741.5	n.125+2659G>C		intron_variant, non_coding_transcript_variant		1
	ENST00000611117.1			downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.0968 AC: 14722 AN: 152134 Hom.: 796 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0809

Gnomad ASJ AF: 0.0323

Gnomad EAS AF: 0.00961

Gnomad SAS AF: 0.0830

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0874

Gnomad OTH AF: 0.0793

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.0969 AC: 14747 AN: 152252 Hom.: 801 Cov.: 32 AF XY: 0.0963 AC XY: 7169 AN XY: 74442

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.0814

Gnomad4 ASJ AF: 0.0323

Gnomad4 EAS AF: 0.00963

Gnomad4 SAS AF: 0.0833

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.0874

Gnomad4 OTH AF: 0.0780

Alfa AF: 0.0455 Hom.: 48

Bravo AF: 0.0970

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.46
DANN	Benign	0.37
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10483140; hg19: chr22-28318192;