6-52247918-T-C

Variant names:

• chr6-52247918-T-C
• rs608137

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

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 0.43 (1388 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: SLC25A20P1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.414
• Publications: 4 publications found

Genes affected

SLC25A20P1 (HGNC:1422): (solute carrier family 25 member 20 pseudogene 1)

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.427 AC: 20261 AN: 47422 Hom.: 1388 Cov.: 0

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.473

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.417

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: 0.427 AC: 20264 AN: 47434 Hom.: 1388 Cov.: 0 AF XY: 0.428 AC XY: 9964 AN XY: 23262

African (AFR) AF: 0.439 AC: 4446 AN: 10138

American (AMR) AF: 0.295 AC: 1637 AN: 5544

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 888 AN: 1718

East Asian (EAS) AF: 0.508 AC: 745 AN: 1466

South Asian (SAS) AF: 0.472 AC: 684 AN: 1448

European-Finnish (FIN) AF: 0.446 AC: 1531 AN: 3434

Middle Eastern (MID) AF: 0.461 AC: 47 AN: 102

European-Non Finnish (NFE) AF: 0.436 AC: 9810 AN: 22484

Other (OTH) AF: 0.419 AC: 294 AN: 702

Alfa AF: 0.643 Hom.: 16947

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.8
DANN	Benign	0.57
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs608137; hg19: chr6-52112716;