rs11691504

Positions:

• chr2-180602462-A-C
• chr2-180602462-A-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/exons	MANE	Protein	UniProt
		n.180602462A>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000225258	ENST00000429816.1	n.235T>G		non_coding_transcript_exon_variant	2/4	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;