2-59773585-T-C

Position:

• chr2-59773585-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000271955	ENST00000606382.1	n.236+53561A>G		intron_variant		5
ENSG00000271955	ENST00000650011.1	n.514-33364A>G		intron_variant

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;