rs211302

Variant names:

• chr10-32056808-C-G
• rs211302
• ENST00000383933.1:n.63C>G

Variant summary

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

The ENST00000383933.1(Y_RNA):​n.63C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 152,208 control chromosomes in the GnomAD database, including 3,303 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 (3300 hom., cov: 32)
  • Exomes 𝑓: 0.26 (3 hom.)
• Consequence: Y_RNA ENST00000383933.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 3 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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.242 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	ENST00000383933.1	n.63C>G		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30446 AN: 152056 Hom.: 3292 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.00789

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.201

GnomAD4 exome AF: 0.265 AC: 9 AN: 34 Hom.: 3 Cov.: 0 AF XY: 0.273 AC XY: 6 AN XY: 22

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.346 AC: 9 AN: 26

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.200 AC: 30490 AN: 152174 Hom.: 3300 Cov.: 32 AF XY: 0.196 AC XY: 14616 AN XY: 74390

African (AFR) AF: 0.161 AC: 6672 AN: 41508

American (AMR) AF: 0.186 AC: 2845 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 814 AN: 3470

East Asian (EAS) AF: 0.00771 AC: 40 AN: 5186

South Asian (SAS) AF: 0.179 AC: 863 AN: 4826

European-Finnish (FIN) AF: 0.182 AC: 1930 AN: 10580

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16658 AN: 67990

Other (OTH) AF: 0.204 AC: 432 AN: 2116

Alfa AF: 0.220 Hom.: 451

Bravo AF: 0.201

Asia WGS AF: 0.122 AC: 425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.7
DANN	Benign	0.42
PhyloP100		-1.1
PromoterAI		-0.0087	Neutral

Splicing

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

Other links and lift over

dbSNP: rs211302; hg19: chr10-32345736;