chr1-40397159-G-A

Position:

• chr1-40397159-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
SMAP2	NM_022733.3	c.104-9577G>A		intron_variant		ENST00000372718.8	NP_073570.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SMAP2	ENST00000372718.8	c.104-9577G>A		intron_variant		1	NM_022733.3	ENSP00000361803	P1

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

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.313

Gnomad4 ASJ AF: 0.446

Gnomad4 EAS AF: 0.357

Gnomad4 SAS AF: 0.402

Gnomad4 FIN AF: 0.403

Gnomad4 NFE AF: 0.484

Gnomad4 OTH AF: 0.394

Alfa AF: 0.454 Hom.: 8893

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs209598; hg19: chr1-40862831;