chr2-203016111-G-C

Variant names:

• chr2-203016111-G-C
• rs4675310
• NM_001378026.1:c.-229-45G>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001378026.1(NBEAL1):​c.-229-45G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: NBEAL1 NM_001378026.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 24 publications found

Genes affected

NBEAL1 (HGNC:20681): (neurobeachin like 1) Predicted to enable protein kinase binding activity. Predicted to be involved in protein localization. Predicted to be active in cytosol and membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001378026.1. 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
	NBEAL1	NM_001378026.1	MANE Select	c.-229-45G>C		intron	N/A	NP_001364955.1	A0A804HKS6
	NBEAL1	NM_001114132.2		c.-229-45G>C		intron	N/A	NP_001107604.1	Q6ZS30-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NBEAL1	ENST00000683969.1	MANE Select	c.-229-45G>C		intron	N/A	ENSP00000508055.1	A0A804HKS6
	NBEAL1	ENST00000478884.5	TSL:1	n.59-45G>C		intron	N/A
	NBEAL1	ENST00000449802.5	TSL:5	c.-229-45G>C		intron	N/A	ENSP00000399903.1	Q6ZS30-2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 137678 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 70672

African (AFR) AF: 0.00 AC: 0 AN: 4506

American (AMR) AF: 0.00 AC: 0 AN: 4576

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 5636

East Asian (EAS) AF: 0.00 AC: 0 AN: 12108

South Asian (SAS) AF: 0.00 AC: 0 AN: 2078

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 7284

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 708

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 91444

Other (OTH) AF: 0.00 AC: 0 AN: 9338

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.81
DANN	Benign	0.41
PhyloP100		-1.2
PromoterAI		-0.0054	Neutral

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs4675310; hg19: chr2-203880834;