rs761167

Variant names:

• chr6-52247010-C-A
• rs761167
• ENST00000408043.1:n.551C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-52247010-C-A
• chr6-52247010-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000408043.1(SLC25A20P1):​n.551C>A 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 0.00000291 in 343,700 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000029 (0 hom.)
• Consequence: SLC25A20P1 ENST00000408043.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.89
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000408043.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC25A20P1	ENST00000408043.1	TSL:6	n.551C>A		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000291 AC: 1 AN: 343700 Hom.: 0 Cov.: 0 AF XY: 0.00000522 AC XY: 1 AN XY: 191564

African (AFR) AF: 0.00 AC: 0 AN: 9314

American (AMR) AF: 0.00 AC: 0 AN: 24576

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9312

East Asian (EAS) AF: 0.00 AC: 0 AN: 15682

South Asian (SAS) AF: 0.0000180 AC: 1 AN: 55632

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 28182

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2516

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 181930

Other (OTH) AF: 0.00 AC: 0 AN: 16556

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	6.1
DANN	Benign	0.67
PhyloP100		2.9

Splicing

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

Other links and lift over

dbSNP: rs761167; hg19: chr6-52111808;