chr15-75351274-C-CTTTTTTT

Variant names:

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

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001352519.2(NEIL1):​c.100-14_100-8dupTTTTTTT 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 0.000033 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00027 (6 hom.)
  • Failed GnomAD Quality Control
• Consequence: NEIL1 NM_001352519.2 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0650
• Publications: 0 publications found

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

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001352519.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NEIL1	NM_024608.4	MANE Select	c.435-824_435-818dupTTTTTTT		intron	N/A	NP_078884.2	Q96FI4
	NEIL1	NM_001256552.1		c.693-824_693-818dupTTTTTTT		intron	N/A	NP_001243481.1	Q96FI4
	NEIL1	NM_001352520.2		c.129-824_129-818dupTTTTTTT		intron	N/A	NP_001339449.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NEIL1	ENST00000355059.9	TSL:2 MANE Select	c.435-837_435-836insTTTTTTT		intron	N/A	ENSP00000347170.4	Q96FI4
	NEIL1	ENST00000569035.5	TSL:1	c.435-837_435-836insTTTTTTT		intron	N/A	ENSP00000455730.1	Q96FI4
	NEIL1	ENST00000866915.1		c.435-837_435-836insTTTTTTT		intron	N/A	ENSP00000536974.1

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

African (AFR) AF: 0.00 AC: 0 AN: 5580

American (AMR) AF: 0.00109 AC: 18 AN: 16534

Ashkenazi Jewish (ASJ) AF: 0.000128 AC: 1 AN: 7802

East Asian (EAS) AF: 0.00280 AC: 23 AN: 8226

South Asian (SAS) AF: 0.000194 AC: 9 AN: 46390

European-Finnish (FIN) AF: 0.000417 AC: 4 AN: 9586

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 846

European-Non Finnish (NFE) AF: 0.0000670 AC: 9 AN: 134384

Other (OTH) AF: 0.00 AC: 0 AN: 11222

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

African (AFR) AF: 0.00 AC: 0 AN: 33298

American (AMR) AF: 0.0000893 AC: 1 AN: 11192

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3114

East Asian (EAS) AF: 0.000512 AC: 2 AN: 3904

South Asian (SAS) AF: 0.00 AC: 0 AN: 3602

European-Finnish (FIN) AF: 0.000242 AC: 1 AN: 4128

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 226

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 59226

Other (OTH) AF: 0.00 AC: 0 AN: 1636

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.065

Splicing

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

Other links and lift over

dbSNP: rs11422837; hg19: chr15-75643615;