rs16839626

Variant names:

• chr2-203225007-G-A
• rs16839626
• NM_001378026.1:c.*7653G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001378026.1(NBEAL1):​c.*7653G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.02 in 152,146 control chromosomes in the GnomAD database, including 99 homozygotes. 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: 𝑓 0.020 (99 hom., cov: 33)
• Consequence: NBEAL1 NM_001378026.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.42
• Publications: 9 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NBEAL1	NM_001378026.1	c.*7653G>A		3_prime_UTR_variant	Exon 56 of 56	ENST00000683969.1	NP_001364955.1
NBEAL1	NM_001114132.2	c.*7653G>A		3_prime_UTR_variant	Exon 55 of 55		NP_001107604.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NBEAL1	ENST00000683969.1	c.*7653G>A		3_prime_UTR_variant	Exon 56 of 56		NM_001378026.1	ENSP00000508055.1
NBEAL1	ENST00000434469.1	c.663-1116G>A		intron_variant	Intron 5 of 5	1		ENSP00000411142.1
NBEAL1	ENST00000684709.1	n.9673G>A		non_coding_transcript_exon_variant	Exon 10 of 10
NBEAL1	ENST00000683650.1	c.*7653G>A		3_prime_UTR_variant	Exon 9 of 9			ENSP00000507863.1

Frequencies

GnomAD3 genomes AF: 0.0199 AC: 3026 AN: 152028 Hom.: 98 Cov.: 33

Gnomad AFR AF: 0.0686

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00864

Gnomad ASJ AF: 0.000576

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00318

Gnomad NFE AF: 0.000235

Gnomad OTH AF: 0.0163

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0200 AC: 3039 AN: 152146 Hom.: 99 Cov.: 33 AF XY: 0.0198 AC XY: 1473 AN XY: 74384

African (AFR) AF: 0.0687 AC: 2853 AN: 41518

American (AMR) AF: 0.00863 AC: 132 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.000576 AC: 2 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5184

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4824

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10582

Middle Eastern (MID) AF: 0.00342 AC: 1 AN: 292

European-Non Finnish (NFE) AF: 0.000235 AC: 16 AN: 67958

Other (OTH) AF: 0.0161 AC: 34 AN: 2110

Alfa AF: 0.0242 Hom.: 61

Bravo AF: 0.0226

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	6.5
DANN	Benign	0.36
PhyloP100		2.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Other links and lift over

dbSNP: rs16839626; hg19: chr2-204089730;