rs2452658

Positions:

• chr8-12551601-A-G
• chr8-12551601-A-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000635775.1(ENSG00000283674):​n.1973-12536T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 (2040 hom., cov: 83)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000283674 ENST00000635775.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0690

Genes affected

ENSG00000283674 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM86B2-DT	NR_040092.1	n.1337-14285A>G		intron_variant
LOC729732	NR_047662.2	n.1996-12536T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000283674	ENST00000635775.1	n.1973-12536T>C		intron_variant		2
ENSG00000283674	ENST00000641618.1	n.587+29227T>C		intron_variant
ENSG00000283674	ENST00000641839.1	n.684-40344T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.00 AC: 74213 AN: 145962 Hom.: 2037 Cov.: 83 FAILED QC

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.509

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.508 AC: 74266 AN: 146060 Hom.: 2040 Cov.: 83 AF XY: 0.510 AC XY: 36420 AN XY: 71410

Gnomad4 AFR AF: 0.508

Gnomad4 AMR AF: 0.517

Gnomad4 ASJ AF: 0.510

Gnomad4 EAS AF: 0.571

Gnomad4 SAS AF: 0.520

Gnomad4 FIN AF: 0.508

Gnomad4 NFE AF: 0.501

Gnomad4 OTH AF: 0.509

Alfa AF: 0.502 Hom.: 232

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.1
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2452658; hg19: chr8-12409110;