rs4872176

Variant names:

• chr8-23680495-C-A
• rs4872176
• NM_006167.4:c.*726G>T

Your query was ambiguous. Multiple possible variants found:

• chr8-23680495-C-A
• chr8-23680495-C-G
• chr8-23680495-C-T

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_006167.4(NKX3-1):​c.*726G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0125 in 152,132 control chromosomes in the GnomAD database, including 25 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 0.013 (25 hom., cov: 32)
  • Exomes 𝑓: 0.031 (0 hom.)
• Consequence: NKX3-1 NM_006167.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150
• Publications: 13 publications found

Genes affected

NKX3-1 (HGNC:7838): (NK3 homeobox 1) This gene encodes a homeobox-containing transcription factor. This transcription factor functions as a negative regulator of epithelial cell growth in prostate tissue. Aberrant expression of this gene is associated with prostate tumor progression. Alternate splicing results in multiple transcript variants of this gene. [provided by RefSeq, Jan 2012]

LOC107986930 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BS2: High Homozygotes in GnomAd4 at 25 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006167.4. 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
	NKX3-1	NM_006167.4	MANE Select	c.*726G>T		3_prime_UTR	Exon 2 of 2	NP_006158.2
	NKX3-1	NR_046072.2		n.683G>T		non_coding_transcript_exon	Exon 2 of 2
	NKX3-1	NM_001256339.1		c.*726G>T		3_prime_UTR	Exon 3 of 3	NP_001243268.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NKX3-1	ENST00000380871.5	TSL:1 MANE Select	c.*726G>T		3_prime_UTR	Exon 2 of 2	ENSP00000370253.4

Frequencies

GnomAD3 genomes AF: 0.0126 AC: 1909 AN: 151982 Hom.: 25 Cov.: 32

Gnomad AFR AF: 0.00334

Gnomad AMI AF: 0.0253

Gnomad AMR AF: 0.0111

Gnomad ASJ AF: 0.0167

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00767

Gnomad FIN AF: 0.0365

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0156

Gnomad OTH AF: 0.0148

GnomAD4 exome AF: 0.0313 AC: 1 AN: 32 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 24

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) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0333 AC: 1 AN: 30

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0125 AC: 1908 AN: 152100 Hom.: 25 Cov.: 32 AF XY: 0.0129 AC XY: 961 AN XY: 74354

African (AFR) AF: 0.00333 AC: 138 AN: 41482

American (AMR) AF: 0.0111 AC: 170 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0167 AC: 58 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5164

South Asian (SAS) AF: 0.00767 AC: 37 AN: 4822

European-Finnish (FIN) AF: 0.0365 AC: 386 AN: 10578

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0156 AC: 1062 AN: 67988

Other (OTH) AF: 0.0147 AC: 31 AN: 2114

Alfa AF: 0.00303 Hom.: 2163

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.0
DANN	Benign	0.40
PhyloP100		0.015
Mutation Taster		=100/0	polymorphism

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: rs4872176; hg19: chr8-23538008;