rs761167

chr6-52247010-C-T

Variant summary

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

The ENST00000408043.1(SLC25A20P1):n.551C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 495,372 control chromosomes in the GnomAD database, including 49,753 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 0.36 (11553 hom., cov: 32)
  • Exomes 𝑓: 0.46 (38200 hom.)
• Consequence: SLC25A20P1 ENST00000408043.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.89

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC25A20P1	ENST00000408043.1	n.551C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55258 AN: 151928 Hom.: 11557 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.384

GnomAD4 exome AF: 0.464 AC: 159457 AN: 343326 Hom.: 38200 Cov.: 0 AF XY: 0.476 AC XY: 91059 AN XY: 191372

Gnomad4 AFR exome AF: 0.159

Gnomad4 AMR exome AF: 0.293

Gnomad4 ASJ exome AF: 0.448

Gnomad4 EAS exome AF: 0.382

Gnomad4 SAS exome AF: 0.517

Gnomad4 FIN exome AF: 0.467

Gnomad4 NFE exome AF: 0.495

Gnomad4 OTH exome AF: 0.460

GnomAD4 genome AF: 0.363 AC: 55255 AN: 152046 Hom.: 11553 Cov.: 32 AF XY: 0.364 AC XY: 27061 AN XY: 74302

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.414

Gnomad4 EAS AF: 0.379

Gnomad4 SAS AF: 0.498

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.385

Alfa AF: 0.454 Hom.: 33200

Bravo AF: 0.342

Asia WGS AF: 0.390 AC: 1357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
Cadd	Benign	9.4
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs761167; hg19: chr6-52111808; COSMIC: COSV60234147;