rs1023568

Variant names:

• chr2-190650716-A-G
• rs1023568
• NM_005966.4:c.-197+734A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-190650716-A-G
• chr2-190650716-A-T

Variant summary

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

The NM_005966.4(NAB1):​c.-197+734A>G 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: 32)
• Consequence: NAB1 NM_005966.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.162
• Publications: 6 publications found

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]

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=-0.51).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005966.4. 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
	NAB1	NM_005966.4	MANE Select	c.-197+734A>G		intron	N/A	NP_005957.2
	NAB1	NM_001321312.2		c.-20+1356A>G		intron	N/A	NP_001308241.1	Q13506-1
	NAB1	NM_001321313.1		c.-20+1745A>G		intron	N/A	NP_001308242.1	Q13506-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAB1	ENST00000337386.10	TSL:1 MANE Select	c.-197+734A>G		intron	N/A	ENSP00000336894.5	Q13506-1
	NAB1	ENST00000903121.1		c.-20+1356A>G		intron	N/A	ENSP00000573180.1
	NAB1	ENST00000409581.5	TSL:2	c.-20+1356A>G		intron	N/A	ENSP00000387089.1	Q13506-1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	13
DANN	Benign	0.92
PhyloP100		0.16

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: rs1023568; hg19: chr2-191515442;