rs4660403

chr1-40348260-G-Achr1-40348260-G-Cchr1-40348260-G-T

Variant summary

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

The ENST00000435168.6(SMAP2):c.-83+3350G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.854 in 152,198 control chromosomes in the GnomAD database, including 55,933 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 0.85 (55933 hom., cov: 33)
• Consequence: SMAP2 ENST00000435168.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.154

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.956 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SMAP2	XM_047428009.1	c.-83+3350G>A		intron_variant
SMAP2	XM_047428011.1	c.-39+3350G>A		intron_variant
SMAP2	XM_047428017.1	c.-138+3350G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SMAP2	ENST00000435168.6	c.-83+3350G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.853 AC: 129785 AN: 152080 Hom.: 55864 Cov.: 33

Gnomad AFR AF: 0.964

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.847

Gnomad ASJ AF: 0.786

Gnomad EAS AF: 0.964

Gnomad SAS AF: 0.886

Gnomad FIN AF: 0.754

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.799

Gnomad OTH AF: 0.840

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

GnomAD4 genome AF: 0.854 AC: 129913 AN: 152198 Hom.: 55933 Cov.: 33 AF XY: 0.851 AC XY: 63349 AN XY: 74404

Gnomad4 AFR AF: 0.964

Gnomad4 AMR AF: 0.847

Gnomad4 ASJ AF: 0.786

Gnomad4 EAS AF: 0.963

Gnomad4 SAS AF: 0.886

Gnomad4 FIN AF: 0.754

Gnomad4 NFE AF: 0.799

Gnomad4 OTH AF: 0.843

Alfa AF: 0.814 Hom.: 26320

Bravo AF: 0.864

Asia WGS AF: 0.932 AC: 3239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.8
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4660403; hg19: chr1-40813932;