rs16896923

Positions:

• chr6-30032910-T-C

Variant summary

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

The ENST00000427296.1(ETF1P1):​n.891T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0629 in 1,025,662 control chromosomes in the GnomAD database, including 2,859 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 0.052 (364 hom., cov: 32)
  • Exomes 𝑓: 0.065 (2495 hom.)
• Consequence: ETF1P1 ENST00000427296.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.201

Genes affected

ETF1P1 (HGNC:3478): (eukaryotic translation termination factor 1 pseudogene 1)

POLR1HASP (HGNC:13924): (POLR1H antisense, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
POLR1HASP	NR_026751.2	n.713+1998A>G		intron_variant, non_coding_transcript_variant
POLR1HASP	NR_145416.1	n.713+1998A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ETF1P1	ENST00000427296.1	n.891T>C		non_coding_transcript_exon_variant	2/2
POLR1HASP	ENST00000688495.1	n.360+25205A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0523 AC: 7952 AN: 152136 Hom.: 363 Cov.: 32

Gnomad AFR AF: 0.0133

Gnomad AMI AF: 0.0980

Gnomad AMR AF: 0.0411

Gnomad ASJ AF: 0.0556

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.0515

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0597

Gnomad OTH AF: 0.0501

GnomAD4 exome AF: 0.0648 AC: 56568 AN: 873408 Hom.: 2495 Cov.: 12 AF XY: 0.0686 AC XY: 31185 AN XY: 454622

Gnomad4 AFR exome AF: 0.0102

Gnomad4 AMR exome AF: 0.0349

Gnomad4 ASJ exome AF: 0.0569

Gnomad4 EAS exome AF: 0.122

Gnomad4 SAS exome AF: 0.149

Gnomad4 FIN exome AF: 0.0489

Gnomad4 NFE exome AF: 0.0573

Gnomad4 OTH exome AF: 0.0647

GnomAD4 genome AF: 0.0522 AC: 7950 AN: 152254 Hom.: 364 Cov.: 32 AF XY: 0.0547 AC XY: 4074 AN XY: 74436

Gnomad4 AFR AF: 0.0133

Gnomad4 AMR AF: 0.0411

Gnomad4 ASJ AF: 0.0556

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.0515

Gnomad4 NFE AF: 0.0597

Gnomad4 OTH AF: 0.0506

Alfa AF: 0.0606 Hom.: 501

Bravo AF: 0.0476

Asia WGS AF: 0.158 AC: 548 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	6.4
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16896923; hg19: chr6-30000687;