6-52246993-C-T

Variant names:

• chr6-52246993-C-T
• rs9463772
• ENST00000408043.1:n.534C>T

Variant summary

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

The ENST00000408043.1(SLC25A20P1):​n.534C>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 0.169 in 504,356 control chromosomes in the GnomAD database, including 7,882 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 0.19 (3225 hom., cov: 32)
  • Exomes 𝑓: 0.16 (4657 hom.)
• Consequence: SLC25A20P1 ENST00000408043.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220
• Publications: 7 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 (AFR) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC25A20P1		n.52246993C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC25A20P1	ENST00000408043.1	n.534C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29513 AN: 151948 Hom.: 3218 Cov.: 32

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.183

GnomAD4 exome AF: 0.158 AC: 55685 AN: 352290 Hom.: 4657 Cov.: 0 AF XY: 0.156 AC XY: 30742 AN XY: 197036

African (AFR) AF: 0.277 AC: 2598 AN: 9364

American (AMR) AF: 0.130 AC: 3269 AN: 25168

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 1849 AN: 9616

East Asian (EAS) AF: 0.142 AC: 2268 AN: 15990

South Asian (SAS) AF: 0.142 AC: 8100 AN: 56900

European-Finnish (FIN) AF: 0.153 AC: 4381 AN: 28646

Middle Eastern (MID) AF: 0.202 AC: 510 AN: 2524

European-Non Finnish (NFE) AF: 0.160 AC: 29887 AN: 187194

Other (OTH) AF: 0.167 AC: 2823 AN: 16888

GnomAD4 genome AF: 0.194 AC: 29547 AN: 152066 Hom.: 3225 Cov.: 32 AF XY: 0.193 AC XY: 14333 AN XY: 74332

African (AFR) AF: 0.280 AC: 11594 AN: 41446

American (AMR) AF: 0.149 AC: 2282 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 718 AN: 3468

East Asian (EAS) AF: 0.140 AC: 723 AN: 5162

South Asian (SAS) AF: 0.133 AC: 642 AN: 4826

European-Finnish (FIN) AF: 0.154 AC: 1634 AN: 10584

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11262 AN: 67970

Other (OTH) AF: 0.182 AC: 386 AN: 2116

Alfa AF: 0.111 Hom.: 220

Bravo AF: 0.200

Asia WGS AF: 0.145 AC: 506 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	5.4
DANN	Benign	0.78
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs9463772; hg19: chr6-52111791; COSMIC: COSV60235672;