6-116249325-A-G

Variant names:

• chr6-116249325-A-G
• rs1204830
• NM_152729.3:c.*5301A>G

Variant summary

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

The NM_152729.3(NT5DC1):​c.*5301A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 152,142 control chromosomes in the GnomAD database, including 4,474 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 0.23 (4474 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: NT5DC1 NM_152729.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.160
• Publications: 4 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152729.3. 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
	NT5DC1	NM_152729.3	MANE Select	c.*5301A>G		3_prime_UTR	Exon 12 of 12	NP_689942.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NT5DC1	ENST00000319550.9	TSL:1 MANE Select	c.*5301A>G		3_prime_UTR	Exon 12 of 12	ENSP00000326858.3

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35587 AN: 152024 Hom.: 4462 Cov.: 33

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.228

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.234 AC: 35639 AN: 152142 Hom.: 4474 Cov.: 33 AF XY: 0.237 AC XY: 17637 AN XY: 74380

African (AFR) AF: 0.300 AC: 12455 AN: 41502

American (AMR) AF: 0.272 AC: 4156 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 927 AN: 3470

East Asian (EAS) AF: 0.311 AC: 1609 AN: 5170

South Asian (SAS) AF: 0.260 AC: 1254 AN: 4822

European-Finnish (FIN) AF: 0.213 AC: 2253 AN: 10590

Middle Eastern (MID) AF: 0.103 AC: 30 AN: 292

European-Non Finnish (NFE) AF: 0.181 AC: 12334 AN: 67982

Other (OTH) AF: 0.232 AC: 491 AN: 2112

Alfa AF: 0.192 Hom.: 2960

Bravo AF: 0.240

Asia WGS AF: 0.346 AC: 1199 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	2.4
DANN	Benign	0.85
PhyloP100		-0.16
Mutation Taster		=100/0	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: rs1204830; hg19: chr6-116570488;