ENST00000429211.2:n.126C>T

Variant names:

• chr1-192800696-C-T
• rs2179652
• ENST00000429211.2:n.126C>T

Variant summary

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

The ENST00000429211.2(ENSG00000226814):​n.126C>T 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 0.559 in 206,522 control chromosomes in the GnomAD database, including 32,369 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 0.56 (23688 hom., cov: 30)
  • Exomes 𝑓: 0.57 (8681 hom.)
• Consequence: ENSG00000226814 ENST00000429211.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.45
• Publications: 8 publications found

Genes affected

ENSG00000226814 (HGNC:):

ENSG00000285280 (HGNC:49018): (RSG2 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100130137		n.192800696C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226814	ENST00000429211.2	n.126C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000285280	ENST00000644058.2	n.202-34502G>A		intron_variant	Intron 1 of 5
ENSG00000285280	ENST00000644134.1	n.105-34502G>A		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84303 AN: 151642 Hom.: 23662 Cov.: 30

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.553

GnomAD4 exome AF: 0.568 AC: 31098 AN: 54762 Hom.: 8681 Cov.: 0 AF XY: 0.571 AC XY: 18458 AN XY: 32344

African (AFR) AF: 0.644 AC: 1084 AN: 1682

American (AMR) AF: 0.506 AC: 3378 AN: 6676

Ashkenazi Jewish (ASJ) AF: 0.636 AC: 476 AN: 748

East Asian (EAS) AF: 0.657 AC: 2356 AN: 3586

South Asian (SAS) AF: 0.627 AC: 4009 AN: 6398

European-Finnish (FIN) AF: 0.478 AC: 2626 AN: 5496

Middle Eastern (MID) AF: 0.655 AC: 1051 AN: 1604

European-Non Finnish (NFE) AF: 0.565 AC: 14952 AN: 26442

Other (OTH) AF: 0.547 AC: 1166 AN: 2130

GnomAD4 genome AF: 0.556 AC: 84375 AN: 151760 Hom.: 23688 Cov.: 30 AF XY: 0.553 AC XY: 40979 AN XY: 74132

African (AFR) AF: 0.620 AC: 25649 AN: 41386

American (AMR) AF: 0.528 AC: 8051 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 2106 AN: 3470

East Asian (EAS) AF: 0.630 AC: 3258 AN: 5170

South Asian (SAS) AF: 0.606 AC: 2910 AN: 4802

European-Finnish (FIN) AF: 0.413 AC: 4337 AN: 10494

Middle Eastern (MID) AF: 0.603 AC: 176 AN: 292

European-Non Finnish (NFE) AF: 0.532 AC: 36107 AN: 67900

Other (OTH) AF: 0.554 AC: 1163 AN: 2098

Alfa AF: 0.549 Hom.: 3443

Bravo AF: 0.563

Asia WGS AF: 0.644 AC: 2236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	1.9
DANN	Benign	0.61
PhyloP100		2.5

Splicing

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

Other links and lift over

dbSNP: rs2179652; hg19: chr1-192769826;