rs10203166

Positions:

• chr2-59562570-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000412409.3(ENSG00000233891):​n.545+32235G>A 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 0.0525 in 152,242 control chromosomes in the GnomAD database, including 361 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 0.052 (361 hom., cov: 32)
• Consequence: ENST00000412409.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.320

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.2).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.115 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
	ENST00000412409.3	n.545+32235G>A		intron_variant, non_coding_transcript_variant		3
	ENST00000606382.1	n.237-50365G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0524 AC: 7967 AN: 152124 Hom.: 356 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0336

Gnomad ASJ AF: 0.0352

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00828

Gnomad FIN AF: 0.0287

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0283

Gnomad OTH AF: 0.0498

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

GnomAD4 genome AF: 0.0525 AC: 7990 AN: 152242 Hom.: 361 Cov.: 32 AF XY: 0.0516 AC XY: 3840 AN XY: 74438

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.0335

Gnomad4 ASJ AF: 0.0352

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00849

Gnomad4 FIN AF: 0.0287

Gnomad4 NFE AF: 0.0283

Gnomad4 OTH AF: 0.0488

Alfa AF: 0.0426 Hom.: 87

Bravo AF: 0.0545

Asia WGS AF: 0.0150 AC: 51 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.20
CADD	Benign	12
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10203166; hg19: chr2-59789705;