rs2179652

Positions:

• chr1-192800696-C-T

Variant summary

Our verdict is Benign. Variant got -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: ENST00000429211.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.45

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000429211.2	n.126C>T		non_coding_transcript_exon_variant	1/1
	ENST00000644134.1	n.105-34502G>A		intron_variant, non_coding_transcript_variant
	ENST00000644058.1	n.194-34502G>A		intron_variant, non_coding_transcript_variant
	ENST00000645822.1	n.200-8228G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR exome AF: 0.644

Gnomad4 AMR exome AF: 0.506

Gnomad4 ASJ exome AF: 0.636

Gnomad4 EAS exome AF: 0.657

Gnomad4 SAS exome AF: 0.627

Gnomad4 FIN exome AF: 0.478

Gnomad4 NFE exome AF: 0.565

Gnomad4 OTH exome AF: 0.547

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

Gnomad4 AFR AF: 0.620

Gnomad4 AMR AF: 0.528

Gnomad4 ASJ AF: 0.607

Gnomad4 EAS AF: 0.630

Gnomad4 SAS AF: 0.606

Gnomad4 FIN AF: 0.413

Gnomad4 NFE AF: 0.532

Gnomad4 OTH AF: 0.554

Alfa AF: 0.547 Hom.: 3300

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2179652; hg19: chr1-192769826;