chr2-180602462-A-C

Variant names:

• chr2-180602462-A-C
• rs11691504
• ENST00000429816.1:n.235T>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000429816.1(ENSG00000225258):​n.235T>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 0.403 in 151,898 control chromosomes in the GnomAD database, including 14,364 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 0.40 (14364 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000225258 ENST00000429816.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.216

Genes affected

ENSG00000225258 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.524 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
ENSG00000225258	ENST00000429816.1	n.235T>G		non_coding_transcript_exon_variant	Exon 2 of 4	3

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61267 AN: 151780 Hom.: 14374 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.466

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.403 AC: 61260 AN: 151898 Hom.: 14364 Cov.: 32 AF XY: 0.399 AC XY: 29592 AN XY: 74224

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.435

Gnomad4 ASJ AF: 0.573

Gnomad4 EAS AF: 0.298

Gnomad4 SAS AF: 0.324

Gnomad4 FIN AF: 0.457

Gnomad4 NFE AF: 0.529

Gnomad4 OTH AF: 0.461

Alfa AF: 0.472 Hom.: 5788

Bravo AF: 0.398

Asia WGS AF: 0.286 AC: 995 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	8.2
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11691504; hg19: chr2-181467189;