chr22-41065861-T-G

Variant names:

• chr22-41065861-T-G
• rs5758209
• ENST00000362645.1:n.-215A>C

Variant summary

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

The ENST00000362645.1(Y_RNA):​n.-215A>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.462 in 151,936 control chromosomes in the GnomAD database, including 16,683 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 0.46 (16683 hom., cov: 31)
• Consequence: Y_RNA ENST00000362645.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.532
• Publications: 15 publications found

Genes affected

Y_RNA (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.716 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
Y_RNA	ENST00000362645.1	n.-215A>C		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.462 AC: 70171 AN: 151818 Hom.: 16647 Cov.: 31

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.462 AC: 70256 AN: 151936 Hom.: 16683 Cov.: 31 AF XY: 0.460 AC XY: 34122 AN XY: 74254

African (AFR) AF: 0.401 AC: 16625 AN: 41420

American (AMR) AF: 0.376 AC: 5730 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1486 AN: 3470

East Asian (EAS) AF: 0.735 AC: 3804 AN: 5174

South Asian (SAS) AF: 0.457 AC: 2197 AN: 4810

European-Finnish (FIN) AF: 0.446 AC: 4710 AN: 10552

Middle Eastern (MID) AF: 0.534 AC: 156 AN: 292

European-Non Finnish (NFE) AF: 0.503 AC: 34150 AN: 67954

Other (OTH) AF: 0.495 AC: 1045 AN: 2112

Alfa AF: 0.485 Hom.: 25428

Bravo AF: 0.454

Asia WGS AF: 0.643 AC: 2235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.87
DANN	Benign	0.75
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs5758209; hg19: chr22-41461865;