rs2577864

Variant names:

• chr12-53893377-C-T
• rs2577864
• ENST00000652339.1:n.510-2820C>T

Variant summary

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

The NR_189097.1(LOC105378250):​n.399-2820C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 152,100 control chromosomes in the GnomAD database, including 11,397 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 0.38 (11397 hom., cov: 32)
• Consequence: LOC105378250 NR_189097.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282

Genes affected

ENSG00000286069 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378250	NR_189097.1	n.399-2820C>T		intron_variant	Intron 2 of 2
LOC105378250	NR_189098.1	n.591-2820C>T		intron_variant	Intron 4 of 4
LOC105378250	NR_189099.1	n.592-2820C>T		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286069	ENST00000652339.1	n.510-2820C>T		intron_variant	Intron 4 of 4
ENSG00000286069	ENST00000654713.1	n.318-2820C>T		intron_variant	Intron 2 of 2
ENSG00000286069	ENST00000656247.1	n.345-2820C>T		intron_variant	Intron 3 of 3
ENSG00000286069	ENST00000663306.1	n.574-2820C>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58149 AN: 151982 Hom.: 11392 Cov.: 32

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.382 AC: 58166 AN: 152100 Hom.: 11397 Cov.: 32 AF XY: 0.375 AC XY: 27850 AN XY: 74356

Gnomad4 AFR AF: 0.414

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.352

Alfa AF: 0.387 Hom.: 1946

Bravo AF: 0.378

Asia WGS AF: 0.296 AC: 1036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.5
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2577864; hg19: chr12-54287161;