2-43772043-C-T

Variant names:

• chr2-43772043-C-T
• rs725238
• ENST00000516681.1:n.*77G>A

Variant summary

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

The ENST00000516681.1(RN7SKP66):​n.*77G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 152,222 control chromosomes in the GnomAD database, including 12,892 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 0.39 (12882 hom., cov: 32)
  • Exomes 𝑓: 0.31 (10 hom.)
• Consequence: RN7SKP66 ENST00000516681.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.424
• Publications: 6 publications found

Genes affected

RN7SKP66 (HGNC:45790): (RN7SK pseudogene 66)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.583 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
RN7SKP66	ENST00000516681.1	n.*77G>A		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58839 AN: 151912 Hom.: 12842 Cov.: 32

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.377

GnomAD4 exome AF: 0.307 AC: 59 AN: 192 Hom.: 10 AF XY: 0.311 AC XY: 46 AN XY: 148

African (AFR) AF: 1.00 AC: 4 AN: 4

American (AMR) AF: 0.500 AC: 1 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.300 AC: 3 AN: 10

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.309 AC: 50 AN: 162

Other (OTH) AF: 0.00 AC: 0 AN: 8

GnomAD4 genome AF: 0.388 AC: 58932 AN: 152030 Hom.: 12882 Cov.: 32 AF XY: 0.387 AC XY: 28773 AN XY: 74338

African (AFR) AF: 0.589 AC: 24407 AN: 41432

American (AMR) AF: 0.426 AC: 6501 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1145 AN: 3468

East Asian (EAS) AF: 0.167 AC: 865 AN: 5166

South Asian (SAS) AF: 0.452 AC: 2175 AN: 4810

European-Finnish (FIN) AF: 0.277 AC: 2925 AN: 10578

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.292 AC: 19832 AN: 67984

Other (OTH) AF: 0.379 AC: 800 AN: 2112

Alfa AF: 0.329 Hom.: 27826

Bravo AF: 0.404

Asia WGS AF: 0.338 AC: 1179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.6
DANN	Benign	0.59
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs725238; hg19: chr2-43999182;