rs1288599

Variant names:

• chr1-53439309-T-C
• rs1288599
• ENST00000566461.2:c.*56+466A>G

Your query was ambiguous. Multiple possible variants found:

• chr1-53439309-T-C
• chr1-53439309-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000566461.2(ENSG00000293253):​c.*56+466A>G variant causes a intron 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: ENSG00000293253 ENST00000566461.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0220
• Publications: 0 publications found

Genes affected

ENSG00000293253 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000566461.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC25A3P1	NR_002314.3		n.247-261A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293253	ENST00000566461.2	TSL:3	c.*56+466A>G		intron	N/A	ENSP00000520458.1
	SLC25A3P1	ENST00000569142.1	TSL:1	n.247-261A>G		intron	N/A
	SLC25A3P1	ENST00000566100.1	TSL:6	n.257A>G		non_coding_transcript_exon	Exon 1 of 1

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

African (AFR) AF: 0.667 AC: 4 AN: 6

American (AMR) AF: 0.500 AC: 2 AN: 4

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.0833 AC: 1 AN: 12

South Asian (SAS) AF: 0.136 AC: 3 AN: 22

European-Finnish (FIN) AF: 0.128 AC: 33 AN: 258

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.207 AC: 98 AN: 474

Other (OTH) AF: 0.227 AC: 5 AN: 22

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

African (AFR) AF: 0.659 AC: 27301 AN: 41450

American (AMR) AF: 0.168 AC: 2564 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 627 AN: 3462

East Asian (EAS) AF: 0.219 AC: 1130 AN: 5168

South Asian (SAS) AF: 0.261 AC: 1262 AN: 4828

European-Finnish (FIN) AF: 0.147 AC: 1563 AN: 10612

Middle Eastern (MID) AF: 0.199 AC: 58 AN: 292

European-Non Finnish (NFE) AF: 0.175 AC: 11913 AN: 67964

Other (OTH) AF: 0.257 AC: 544 AN: 2114

Alfa AF: 0.257 Hom.: 968

Bravo AF: 0.323

Asia WGS AF: 0.233 AC: 812 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	9.7
DANN	Benign	0.18
PhyloP100		0.022
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1288599; hg19: chr1-53904982;