6-116247610-A-C

Position:

• chr6-116247610-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152729.3(NT5DC1):​c.*3586A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 152,084 control chromosomes in the GnomAD database, including 9,257 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 0.32 (9257 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: NT5DC1 NM_152729.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.495

Genes affected

NT5DC1 (HGNC:21556): (5'-nucleotidase domain containing 1) While the exact function of the protein encoded by this gene is not known, it belongs to the 5'(3')-deoxyribonucleotidase family. [provided by RefSeq, May 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.641 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NT5DC1	NM_152729.3	c.*3586A>C		3_prime_UTR_variant	12/12	ENST00000319550.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NT5DC1	ENST00000319550.9	c.*3586A>C		3_prime_UTR_variant	12/12	1	NM_152729.3	P1

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48534 AN: 151968 Hom.: 9250 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.659

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.332

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.319 AC: 48559 AN: 152084 Hom.: 9257 Cov.: 32 AF XY: 0.327 AC XY: 24334 AN XY: 74336

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.375

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.659

Gnomad4 SAS AF: 0.541

Gnomad4 FIN AF: 0.420

Gnomad4 NFE AF: 0.370

Gnomad4 OTH AF: 0.333

Alfa AF: 0.267 Hom.: 1037

Bravo AF: 0.307

Asia WGS AF: 0.491 AC: 1709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.62
DANN	Benign	0.74

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

Publications

LitVar

Other links and lift over

dbSNP: rs1052443; hg19: chr6-116568773; COSMIC: COSV60307281; COSMIC: COSV60307281;