15-75351274-CTTTTTTTTT-CTTTTTTTTTTTTT

Variant names:

• chr15-75351274-C-CTTTT
• rs11422837
• NM_024608.4:c.435-821_435-818dupTTTT

Variant summary

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

The NM_001352519.2(NEIL1):​c.100-11_100-8dupTTTT variant causes a splice region, 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 0.00012 (1 hom., cov: 0)
  • Exomes 𝑓: 0.0017 (1 hom.)
• Consequence: NEIL1 NM_001352519.2 splice_region, 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.435-821_435-818dupTTTT		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_435-836insTTTT		intron_variant	Intron 2 of 9	2	NM_024608.4	ENSP00000347170.4

Frequencies

GnomAD3 genomes AF: 0.000116 AC: 14 AN: 121132 Hom.: 1 Cov.: 0

Gnomad AFR AF: 0.000150

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000510

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000484

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000675

Gnomad OTH AF: 0.000617

GnomAD4 exome AF: 0.00167 AC: 402 AN: 240198 Hom.: 1 Cov.: 0 AF XY: 0.00168 AC XY: 232 AN XY: 138262

Gnomad4 AFR exome AF: 0.000896

Gnomad4 AMR exome AF: 0.00540

Gnomad4 ASJ exome AF: 0.000770

Gnomad4 EAS exome AF: 0.0154

Gnomad4 SAS exome AF: 0.000950

Gnomad4 FIN exome AF: 0.00251

Gnomad4 NFE exome AF: 0.000715

Gnomad4 OTH exome AF: 0.000981

GnomAD4 genome AF: 0.000116 AC: 14 AN: 121126 Hom.: 1 Cov.: 0 AF XY: 0.000124 AC XY: 7 AN XY: 56382

Gnomad4 AFR AF: 0.000150

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000512

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000484

Gnomad4 NFE AF: 0.0000675

Gnomad4 OTH AF: 0.000611

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;