rs2561893

chr2-59333279-T-C

Variant summary

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

The ENST00000412409.3(ENSG00000233891):n.546-92176A>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 0.318 in 152,078 control chromosomes in the GnomAD database, including 8,151 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 0.32 (8151 hom., cov: 32)
• Consequence: ENST00000412409.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.49

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374754	XR_002959389.2	n.1447+54783A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000412409.3	n.546-92176A>G		intron_variant, non_coding_transcript_variant		3
	ENST00000606382.1	n.434-114555A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48398 AN: 151958 Hom.: 8155 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.318 AC: 48412 AN: 152078 Hom.: 8151 Cov.: 32 AF XY: 0.323 AC XY: 24006 AN XY: 74344

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.447

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.489

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.332

Gnomad4 OTH AF: 0.330

Alfa AF: 0.260 Hom.: 1322

Bravo AF: 0.326

Asia WGS AF: 0.387 AC: 1347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
Cadd	Benign	19
Dann	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2561893; hg19: chr2-59560414;