15-75351274-CTTTTTTTTT-CTTTTTTTTTTTTTTT

Variant names:

• chr15-75351274-C-CTTTTTT
• rs11422837
• NM_024608.4:c.435-823_435-818dupTTTTTT

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_001352519.2(NEIL1):​c.100-13_100-8dupTTTTTT 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 0.00016 (1 hom., cov: 0)
  • Exomes 𝑓: 0.00088 (3 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 Likely_benign. Variant got -4 ACMG points.

• BS2: High Homozygotes in GnomAdExome4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NEIL1	NM_024608.4	c.435-823_435-818dupTTTTTT		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_435-836insTTTTTT		intron_variant	Intron 2 of 9	2	NM_024608.4	ENSP00000347170.4

Frequencies

GnomAD3 genomes AF: 0.000165 AC: 20 AN: 121146 Hom.: 1 Cov.: 0

Gnomad AFR AF: 0.0000301

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000179

Gnomad ASJ AF: 0.000321

Gnomad EAS AF: 0.00204

Gnomad SAS AF: 0.000830

Gnomad FIN AF: 0.000242

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000338

Gnomad OTH AF: 0.00123

GnomAD4 exome AF: 0.000882 AC: 212 AN: 240492 Hom.: 3 Cov.: 0 AF XY: 0.000759 AC XY: 105 AN XY: 138428

Gnomad4 AFR exome AF: 0.000537

Gnomad4 AMR exome AF: 0.00351

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0103

Gnomad4 SAS exome AF: 0.000668

Gnomad4 FIN exome AF: 0.000939

Gnomad4 NFE exome AF: 0.000127

Gnomad4 OTH exome AF: 0.000891

GnomAD4 genome AF: 0.000157 AC: 19 AN: 121140 Hom.: 1 Cov.: 0 AF XY: 0.000160 AC XY: 9 AN XY: 56386

Gnomad4 AFR AF: 0.0000300

Gnomad4 AMR AF: 0.000179

Gnomad4 ASJ AF: 0.000321

Gnomad4 EAS AF: 0.00179

Gnomad4 SAS AF: 0.000833

Gnomad4 FIN AF: 0.000242

Gnomad4 NFE AF: 0.0000338

Gnomad4 OTH AF: 0.00122

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;