chr1-53439309-T-C

Position:

• chr1-53439309-T-C

Variant summary

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

The NR_002314.3(SLC25A3P1):​n.247-261A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 152,902 control chromosomes in the GnomAD database, including 10,871 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 0.31 (10854 hom., cov: 33)
  • Exomes 𝑓: 0.18 (17 hom.)
• Consequence: SLC25A3P1 NR_002314.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0220

Genes affected

SLC25A3P1 (HGNC:26869): (solute carrier family 25 member 3 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC25A3P1	NR_002314.3	n.247-261A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC25A3P1	ENST00000563752.5	n.201+466A>G		intron_variant, non_coding_transcript_variant		2
SLC25A3P1	ENST00000443844.3			upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46994 AN: 151982 Hom.: 10810 Cov.: 33

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.258

GnomAD4 exome AF: 0.182 AC: 146 AN: 802 Hom.: 17 Cov.: 0 AF XY: 0.181 AC XY: 108 AN XY: 596

Gnomad4 AFR exome AF: 0.667

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0833

Gnomad4 SAS exome AF: 0.136

Gnomad4 FIN exome AF: 0.128

Gnomad4 NFE exome AF: 0.207

Gnomad4 OTH exome AF: 0.227

GnomAD4 genome AF: 0.310 AC: 47084 AN: 152100 Hom.: 10854 Cov.: 33 AF XY: 0.304 AC XY: 22605 AN XY: 74346

Gnomad4 AFR AF: 0.659

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.219

Gnomad4 SAS AF: 0.261

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.257

Alfa AF: 0.240 Hom.: 805

Bravo AF: 0.323

Asia WGS AF: 0.233 AC: 812 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	9.7
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1288599; hg19: chr1-53904982;