1-40412836-C-T

Variant names:

• chr1-40412836-C-T
• rs209603
• NM_022733.3:c.403-180C>T

Variant summary

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

The NM_022733.3(SMAP2):​c.403-180C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.91 in 152,190 control chromosomes in the GnomAD database, including 63,322 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 0.91 (63322 hom., cov: 30)
• Consequence: SMAP2 NM_022733.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.352
• Publications: 2 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.97 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMAP2	NM_022733.3	c.403-180C>T		intron_variant	Intron 4 of 9	ENST00000372718.8	NP_073570.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMAP2	ENST00000372718.8	c.403-180C>T		intron_variant	Intron 4 of 9	1	NM_022733.3	ENSP00000361803.3

Frequencies

GnomAD3 genomes AF: 0.910 AC: 138451 AN: 152072 Hom.: 63267 Cov.: 30

Gnomad AFR AF: 0.978

Gnomad AMI AF: 0.913

Gnomad AMR AF: 0.927

Gnomad ASJ AF: 0.931

Gnomad EAS AF: 0.967

Gnomad SAS AF: 0.925

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.879

Gnomad OTH AF: 0.920

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

GnomAD4 genome AF: 0.910 AC: 138564 AN: 152190 Hom.: 63322 Cov.: 30 AF XY: 0.907 AC XY: 67478 AN XY: 74400

African (AFR) AF: 0.978 AC: 40623 AN: 41530

American (AMR) AF: 0.927 AC: 14179 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.931 AC: 3230 AN: 3470

East Asian (EAS) AF: 0.967 AC: 4993 AN: 5166

South Asian (SAS) AF: 0.925 AC: 4455 AN: 4816

European-Finnish (FIN) AF: 0.782 AC: 8273 AN: 10578

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.879 AC: 59761 AN: 68016

Other (OTH) AF: 0.920 AC: 1944 AN: 2114

Alfa AF: 0.888 Hom.: 4798

Bravo AF: 0.922

Asia WGS AF: 0.941 AC: 3273 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	0.78
DANN	Benign	0.72
PhyloP100		-0.35
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: rs209603; hg19: chr1-40878508;