ENST00000365328.1:n.-43C>T

Variant names:

• chr6-52995577-C-T
• rs16883343
• ENST00000365328.1:n.-43C>T

Variant summary

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

The ENST00000365328.1(7SK):​n.-43C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 165,814 control chromosomes in the GnomAD database, including 5,852 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 0.26 (5497 hom., cov: 33)
  • Exomes 𝑓: 0.22 (355 hom.)
• Consequence: 7SK ENST00000365328.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.78
• Publications: 10 publications found

Genes affected

7SK (HGNC:):

RN7SK (HGNC:10037): (RNA component of 7SK nuclear ribonucleoprotein)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000365328.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RN7SK	NR_001445.2		n.-43C>T		upstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	7SK	ENST00000365328.1	TSL:6	n.-43C>T		upstream_gene	N/A
	RN7SK	ENST00000636484.1	TSL:6	n.-44C>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39721 AN: 151838 Hom.: 5477 Cov.: 33

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.256

GnomAD4 exome AF: 0.219 AC: 3029 AN: 13858 Hom.: 355 Cov.: 0 AF XY: 0.219 AC XY: 1427 AN XY: 6502

African (AFR) AF: 0.331 AC: 149 AN: 450

American (AMR) AF: 0.190 AC: 51 AN: 268

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 229 AN: 874

East Asian (EAS) AF: 0.139 AC: 435 AN: 3124

South Asian (SAS) AF: 0.113 AC: 12 AN: 106

European-Finnish (FIN) AF: 0.224 AC: 51 AN: 228

Middle Eastern (MID) AF: 0.337 AC: 31 AN: 92

European-Non Finnish (NFE) AF: 0.239 AC: 1827 AN: 7644

Other (OTH) AF: 0.228 AC: 244 AN: 1072

GnomAD4 genome AF: 0.262 AC: 39772 AN: 151956 Hom.: 5497 Cov.: 33 AF XY: 0.256 AC XY: 19043 AN XY: 74278

African (AFR) AF: 0.342 AC: 14174 AN: 41504

American (AMR) AF: 0.219 AC: 3341 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1087 AN: 3460

East Asian (EAS) AF: 0.132 AC: 684 AN: 5174

South Asian (SAS) AF: 0.157 AC: 756 AN: 4818

European-Finnish (FIN) AF: 0.207 AC: 2195 AN: 10584

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.247 AC: 16744 AN: 67832

Other (OTH) AF: 0.253 AC: 535 AN: 2112

Alfa AF: 0.210 Hom.: 1705

Bravo AF: 0.267

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.0010
DANN	Benign	0.74
PhyloP100		-5.8
PromoterAI		-0.059	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs16883343;

hg19: chr6-52860375;