6-52247010-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

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>T		non_coding_transcript_exon	Exon 1 of 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

African (AFR) AF: 0.159 AC: 1479 AN: 9312

American (AMR) AF: 0.293 AC: 7187 AN: 24554

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 4165 AN: 9294

East Asian (EAS) AF: 0.382 AC: 5984 AN: 15660

South Asian (SAS) AF: 0.517 AC: 28724 AN: 55612

European-Finnish (FIN) AF: 0.467 AC: 13119 AN: 28118

Middle Eastern (MID) AF: 0.482 AC: 1213 AN: 2516

European-Non Finnish (NFE) AF: 0.495 AC: 89986 AN: 181732

Other (OTH) AF: 0.460 AC: 7600 AN: 16528

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

African (AFR) AF: 0.149 AC: 6192 AN: 41502

American (AMR) AF: 0.324 AC: 4946 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 1437 AN: 3470

East Asian (EAS) AF: 0.379 AC: 1957 AN: 5166

South Asian (SAS) AF: 0.498 AC: 2393 AN: 4806

European-Finnish (FIN) AF: 0.448 AC: 4717 AN: 10538

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.475 AC: 32284 AN: 67980

Other (OTH) AF: 0.385 AC: 814 AN: 2114

Alfa AF: 0.431 Hom.: 49543

Bravo AF: 0.342

Asia WGS AF: 0.390 AC: 1357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	9.4
DANN	Benign	0.74
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; COSMIC: COSV60234147;