2-59773585-T-C

Variant names:

• chr2-59773585-T-C
• rs2192512
• ENST00000606382.1:n.236+53561A>G

Variant summary

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

The ENST00000606382.1(ENSG00000271955):​n.236+53561A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 151,932 control chromosomes in the GnomAD database, including 19,652 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 0.51 (19652 hom., cov: 32)
• Consequence: ENSG00000271955 ENST00000606382.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125

Genes affected

ENSG00000271955 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000271955	ENST00000606382.1	n.236+53561A>G		intron_variant	Intron 2 of 3	5
ENSG00000271955	ENST00000650011.1	n.514-33364A>G		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77051 AN: 151814 Hom.: 19619 Cov.: 32

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.508 AC: 77124 AN: 151932 Hom.: 19652 Cov.: 32 AF XY: 0.512 AC XY: 38028 AN XY: 74276

Gnomad4 AFR AF: 0.499

Gnomad4 AMR AF: 0.553

Gnomad4 ASJ AF: 0.525

Gnomad4 EAS AF: 0.571

Gnomad4 SAS AF: 0.590

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.538

Alfa AF: 0.511 Hom.: 3161

Bravo AF: 0.507

Asia WGS AF: 0.601 AC: 2087 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.0
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2192512; hg19: chr2-60000720;