rs10180522

Positions:

• chr2-145314285-A-C

Variant summary

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

The ENST00000454965.1(ENSG00000235435):​n.126+11121T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 152,064 control chromosomes in the GnomAD database, including 5,220 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 0.25 (5220 hom., cov: 32)
• Consequence: ENST00000454965.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000454965.1	n.126+11121T>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37998 AN: 151946 Hom.: 5221 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.262

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.250 AC: 37991 AN: 152064 Hom.: 5220 Cov.: 32 AF XY: 0.249 AC XY: 18508 AN XY: 74332

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.272

Gnomad4 ASJ AF: 0.338

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.262

Alfa AF: 0.295 Hom.: 6665

Bravo AF: 0.243

Asia WGS AF: 0.214 AC: 745 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10180522; hg19: chr2-146071853;