rs7639267

Variant names:

• chr3-52534789-G-T
• rs7639267
• ENST00000492555.5:n.-136C>A

Variant summary

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

The ENST00000492555.5(NT5DC2):​n.-136C>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 0.552 in 1,111,396 control chromosomes in the GnomAD database, including 172,965 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 0.59 (26515 hom., cov: 33)
  • Exomes 𝑓: 0.55 (146450 hom.)
• Consequence: NT5DC2 ENST00000492555.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160
• Publications: 22 publications found

Genes affected

NT5DC2 (HGNC:25717): (5'-nucleotidase domain containing 2) Predicted to enable 5'-nucleotidase activity. Predicted to be involved in dephosphorylation. [provided by Alliance of Genome Resources, Apr 2022]

UQCC5 (HGNC:37257): (ubiquinol-cytochrome c reductase complex assembly factor 5) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000492555.5. 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
	NT5DC2	NM_022908.3		c.-136C>A		5_prime_UTR	Exon 1 of 14	NP_075059.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NT5DC2	ENST00000492555.5	TSL:1	n.-136C>A		non_coding_transcript_exon	Exon 1 of 13	ENSP00000419774.1
	NT5DC2	ENST00000492555.5	TSL:1	n.-136C>A		5_prime_UTR	Exon 1 of 13	ENSP00000419774.1
	UQCC5	ENST00000482728.1	TSL:2	n.265G>T		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.586 AC: 88968 AN: 151944 Hom.: 26477 Cov.: 33

Gnomad AFR AF: 0.657

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.579

GnomAD4 exome AF: 0.547 AC: 524569 AN: 959334 Hom.: 146450 Cov.: 13 AF XY: 0.539 AC XY: 261009 AN XY: 484374

African (AFR) AF: 0.668 AC: 15168 AN: 22722

American (AMR) AF: 0.650 AC: 18824 AN: 28946

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 9721 AN: 17628

East Asian (EAS) AF: 0.493 AC: 18164 AN: 36872

South Asian (SAS) AF: 0.339 AC: 21271 AN: 62706

European-Finnish (FIN) AF: 0.554 AC: 19207 AN: 34696

Middle Eastern (MID) AF: 0.532 AC: 2097 AN: 3944

European-Non Finnish (NFE) AF: 0.560 AC: 396833 AN: 708696

Other (OTH) AF: 0.540 AC: 23284 AN: 43124

GnomAD4 genome AF: 0.586 AC: 89065 AN: 152062 Hom.: 26515 Cov.: 33 AF XY: 0.581 AC XY: 43187 AN XY: 74324

African (AFR) AF: 0.658 AC: 27270 AN: 41468

American (AMR) AF: 0.643 AC: 9828 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1913 AN: 3468

East Asian (EAS) AF: 0.452 AC: 2338 AN: 5168

South Asian (SAS) AF: 0.333 AC: 1608 AN: 4824

European-Finnish (FIN) AF: 0.545 AC: 5751 AN: 10560

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.565 AC: 38427 AN: 67972

Other (OTH) AF: 0.583 AC: 1230 AN: 2108

Alfa AF: 0.584 Hom.: 13880

Bravo AF: 0.600

Asia WGS AF: 0.456 AC: 1590 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.6
DANN	Benign	0.63
PhyloP100		-0.016
PromoterAI		0.013	Neutral
Mutation Taster		=300/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs7639267; hg19: chr3-52568805;