NM_024608.4:c.435-824_435-818dupTTTTTTT

Variant names:

• chr15-75351274-C-CTTTTTTT
• rs11422837
• NM_024608.4:c.435-824_435-818dupTTTTTTT

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_024608.4(NEIL1):​c.435-824_435-818dupTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000033 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00027 (6 hom.)
  • Failed GnomAD Quality Control
• Consequence: NEIL1 NM_024608.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0650

Genes affected

NEIL1 (HGNC:18448): (nei like DNA glycosylase 1) This gene is a member of the Nei endonuclease VIII-like gene family which encodes DNA glycosylases. The encoded enzyme participates in the DNA repair pathway by initiating base excision repair by removing damaged bases, primarily oxidized pyrimidines. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2012]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NEIL1	NM_024608.4	c.435-824_435-818dupTTTTTTT		intron_variant	Intron 2 of 9	ENST00000355059.9	NP_078884.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NEIL1	ENST00000355059.9	c.435-837_435-836insTTTTTTT		intron_variant	Intron 2 of 9	2	NM_024608.4	ENSP00000347170.4

Frequencies

GnomAD3 genomes AF: 0.0000330 AC: 4 AN: 121146 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000894

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000510

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000242

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000266 AC: 64 AN: 240570 Hom.: 6 Cov.: 0 AF XY: 0.000274 AC XY: 38 AN XY: 138470

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00109

Gnomad4 ASJ exome AF: 0.000128

Gnomad4 EAS exome AF: 0.00280

Gnomad4 SAS exome AF: 0.000194

Gnomad4 FIN exome AF: 0.000417

Gnomad4 NFE exome AF: 0.0000670

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0000330 AC: 4 AN: 121140 Hom.: 0 Cov.: 0 AF XY: 0.0000532 AC XY: 3 AN XY: 56384

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.0000893

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000512

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000242

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11422837; hg19: chr15-75643615;