rs3763398

Variant names:

• chr7-128344221-C-T
• rs3763398
• ENST00000459281.1:n.*79C>T

Variant summary

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

The ENST00000459281.1(RNU7-27P):​n.*79C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,830 control chromosomes in the GnomAD database, including 3,252 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 0.20 (3236 hom., cov: 33)
  • Exomes 𝑓: 0.19 (16 hom.)
• Consequence: RNU7-27P ENST00000459281.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600
• Publications: 2 publications found

Genes affected

RNU7-27P (HGNC:34123): (RNA, U7 small nuclear 27 pseudogene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RNU7-27P	ENST00000459281.1	n.*79C>T		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30158 AN: 152022 Hom.: 3235 Cov.: 33

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.232

GnomAD4 exome AF: 0.193 AC: 133 AN: 690 Hom.: 16 AF XY: 0.194 AC XY: 66 AN XY: 340

African (AFR) AF: 0.0750 AC: 3 AN: 40

American (AMR) AF: 0.308 AC: 8 AN: 26

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 9 AN: 46

East Asian (EAS) AF: 0.0833 AC: 1 AN: 12

South Asian (SAS) AF: 0.291 AC: 25 AN: 86

European-Finnish (FIN) AF: 0.188 AC: 3 AN: 16

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.183 AC: 80 AN: 436

Other (OTH) AF: 0.154 AC: 4 AN: 26

GnomAD4 genome AF: 0.198 AC: 30163 AN: 152140 Hom.: 3236 Cov.: 33 AF XY: 0.201 AC XY: 14917 AN XY: 74366

African (AFR) AF: 0.131 AC: 5448 AN: 41500

American (AMR) AF: 0.210 AC: 3209 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 869 AN: 3470

East Asian (EAS) AF: 0.143 AC: 740 AN: 5174

South Asian (SAS) AF: 0.326 AC: 1571 AN: 4820

European-Finnish (FIN) AF: 0.223 AC: 2362 AN: 10572

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15290 AN: 67982

Other (OTH) AF: 0.231 AC: 489 AN: 2116

Alfa AF: 0.222 Hom.: 5522

Bravo AF: 0.195

Asia WGS AF: 0.232 AC: 807 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.7
DANN	Benign	0.79
PhyloP100		0.0060
PromoterAI		0.0045	Neutral
Mutation Taster		=97/3	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs3763398; hg19: chr7-127984275;