chr4-177366124-A-G

Variant names:

• chr4-177366124-A-G
• rs7689397
• XM_047415894.1:c.*1205+2448A>G

Variant summary

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

The XR_001741926.2(LOC105377558):​n.37-4752T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.831 in 152,102 control chromosomes in the GnomAD database, including 53,455 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 0.83 (53455 hom., cov: 33)
• Consequence: LOC105377558 XR_001741926.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.321
• Publications: 4 publications found

Genes affected

NEIL3 (HGNC:24573): (nei like DNA glycosylase 3) NEIL3 belongs to a class of DNA glycosylases homologous to the bacterial Fpg/Nei family. These glycosylases initiate the first step in base excision repair by cleaving bases damaged by reactive oxygen species and introducing a DNA strand break via the associated lyase reaction (Bandaru et al., 2002 [PubMed 12509226]).[supplied by OMIM, Mar 2008]

LOC105377558 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.832 AC: 126420 AN: 151984 Hom.: 53446 Cov.: 33

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.965

Gnomad AMR AF: 0.870

Gnomad ASJ AF: 0.836

Gnomad EAS AF: 0.854

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.942

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.904

Gnomad OTH AF: 0.840

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.831 AC: 126470 AN: 152102 Hom.: 53455 Cov.: 33 AF XY: 0.832 AC XY: 61827 AN XY: 74334

African (AFR) AF: 0.668 AC: 27714 AN: 41468

American (AMR) AF: 0.870 AC: 13305 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.836 AC: 2897 AN: 3464

East Asian (EAS) AF: 0.853 AC: 4415 AN: 5176

South Asian (SAS) AF: 0.784 AC: 3777 AN: 4820

European-Finnish (FIN) AF: 0.942 AC: 9982 AN: 10596

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.904 AC: 61475 AN: 67974

Other (OTH) AF: 0.841 AC: 1777 AN: 2114

Alfa AF: 0.868 Hom.: 18266

Bravo AF: 0.822

Asia WGS AF: 0.819 AC: 2849 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.0
DANN	Benign	0.72
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs7689397; hg19: chr4-178287278;