rs209598

Variant names:

• chr1-40397159-G-A
• rs209598
• NM_022733.3:c.104-9577G>A

Variant summary

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

The NM_022733.3(SMAP2):​c.104-9577G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 151,922 control chromosomes in the GnomAD database, including 12,635 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 0.40 (12635 hom., cov: 31)
• Consequence: SMAP2 NM_022733.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110
• Publications: 8 publications found

Genes affected

SMAP2 (HGNC:25082): (small ArfGAP2) Predicted to enable GTPase activator activity. Predicted to be involved in regulation of catalytic activity. Predicted to be located in cytoplasm. [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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMAP2	NM_022733.3	c.104-9577G>A		intron_variant	Intron 1 of 9	ENST00000372718.8	NP_073570.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMAP2	ENST00000372718.8	c.104-9577G>A		intron_variant	Intron 1 of 9	1	NM_022733.3	ENSP00000361803.3

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60220 AN: 151802 Hom.: 12634 Cov.: 31

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.397 AC: 60247 AN: 151922 Hom.: 12635 Cov.: 31 AF XY: 0.392 AC XY: 29071 AN XY: 74250

African (AFR) AF: 0.279 AC: 11552 AN: 41414

American (AMR) AF: 0.313 AC: 4778 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.446 AC: 1547 AN: 3468

East Asian (EAS) AF: 0.357 AC: 1841 AN: 5164

South Asian (SAS) AF: 0.402 AC: 1940 AN: 4826

European-Finnish (FIN) AF: 0.403 AC: 4241 AN: 10520

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.484 AC: 32868 AN: 67934

Other (OTH) AF: 0.394 AC: 833 AN: 2112

Alfa AF: 0.455 Hom.: 9846

Bravo AF: 0.379

Asia WGS AF: 0.383 AC: 1333 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.8
DANN	Benign	0.79
PhyloP100		-0.011
PromoterAI		-0.035	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs209598; hg19: chr1-40862831;