17-77920078-C-T

Variant names:

• chr17-77920078-C-T
• rs9902857
• ENST00000722557.1:n.245-10352G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000722557.1(ENSG00000294294):​n.245-10352G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,058 control chromosomes in the GnomAD database, including 4,838 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 0.24 (4838 hom., cov: 31)
  • Exomes 𝑓: 0.33 (0 hom.)
• Consequence: ENSG00000294294 ENST00000722557.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 3 publications found

Genes affected

ENSG00000294294 (HGNC:):

RNU1-80P (HGNC:48422): (RNA, U1 small nuclear 80, pseudogene)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000722557.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294294	ENST00000722557.1		n.245-10352G>A		intron	N/A
	RNU1-80P	ENST00000459500.1	TSL:6	n.-20C>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36286 AN: 151934 Hom.: 4833 Cov.: 31

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.0520

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.242

GnomAD4 exome AF: 0.333 AC: 2 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.333 AC XY: 2 AN XY: 6

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.239 AC: 36326 AN: 152052 Hom.: 4838 Cov.: 31 AF XY: 0.236 AC XY: 17542 AN XY: 74324

African (AFR) AF: 0.358 AC: 14822 AN: 41454

American (AMR) AF: 0.198 AC: 3029 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 962 AN: 3466

East Asian (EAS) AF: 0.0522 AC: 270 AN: 5176

South Asian (SAS) AF: 0.193 AC: 930 AN: 4818

European-Finnish (FIN) AF: 0.180 AC: 1900 AN: 10562

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13499 AN: 67978

Other (OTH) AF: 0.244 AC: 514 AN: 2106

Alfa AF: 0.212 Hom.: 14460

Bravo AF: 0.247

Asia WGS AF: 0.142 AC: 494 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.028
DANN	Benign	0.42
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs9902857; hg19: chr17-75916160;