rs10931468

chr2-190673836-C-Achr2-190673836-C-Gchr2-190673836-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005966.4(NAB1):c.1005+684C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,072 control chromosomes in the GnomAD database, including 2,887 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 0.18 (2887 hom., cov: 32)
• Consequence: NAB1 NM_005966.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.232

Genes affected

NAB1 (HGNC:7626): (NGFI-A binding protein 1) Predicted to enable transcription coregulator activity. Predicted to be involved in regulation of transcription, DNA-templated. Predicted to act upstream of or within endochondral ossification; nervous system development; and regulation of epidermis development. Predicted to be located in nucleoplasm. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NAB1	NM_005966.4	c.1005+684C>A		intron_variant		ENST00000337386.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NAB1	ENST00000337386.10	c.1005+684C>A		intron_variant		1	NM_005966.4	P4
	ENST00000676095.2	n.968-1309G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27617 AN: 151954 Hom.: 2877 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.0989

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.182 AC: 27651 AN: 152072 Hom.: 2887 Cov.: 32 AF XY: 0.186 AC XY: 13829 AN XY: 74330

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.0989

Gnomad4 EAS AF: 0.402

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.173

Alfa AF: 0.144 Hom.: 4098

Bravo AF: 0.195

Asia WGS AF: 0.287 AC: 999 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.52
Dann	Benign	0.64

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

Publications

LitVar

Other links and lift over

dbSNP: rs10931468; hg19: chr2-191538562;