rs7140285

Variant names:

• chr14-87996644-C-T
• rs7140285
• ENST00000516974.1:n.-196G>A

Variant summary

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

The ENST00000516974.1(RNU6-835P):​n.-196G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0845 in 151,870 control chromosomes in the GnomAD database, including 638 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 0.085 (638 hom., cov: 33)
• Consequence: RNU6-835P ENST00000516974.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.995
• Publications: 8 publications found

Genes affected

RNU6-835P (HGNC:47798): (RNA, U6 small nuclear 835, pseudogene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.117 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
RNU6-835P	ENST00000516974.1	n.-196G>A		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.0846 AC: 12836 AN: 151752 Hom.: 636 Cov.: 33

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.0614

Gnomad ASJ AF: 0.0473

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0588

Gnomad FIN AF: 0.0779

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0789

Gnomad OTH AF: 0.0800

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0845 AC: 12837 AN: 151870 Hom.: 638 Cov.: 33 AF XY: 0.0818 AC XY: 6070 AN XY: 74238

African (AFR) AF: 0.120 AC: 4978 AN: 41384

American (AMR) AF: 0.0612 AC: 935 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0473 AC: 164 AN: 3470

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5168

South Asian (SAS) AF: 0.0586 AC: 283 AN: 4828

European-Finnish (FIN) AF: 0.0779 AC: 816 AN: 10480

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0789 AC: 5364 AN: 67956

Other (OTH) AF: 0.0787 AC: 166 AN: 2110

Alfa AF: 0.0796 Hom.: 658

Bravo AF: 0.0853

Asia WGS AF: 0.0340 AC: 120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	4.3
DANN	Benign	0.46
PhyloP100		0.99

Splicing

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

Other links and lift over

dbSNP: rs7140285; hg19: chr14-88462988;