rs4660403

Variant names:

• chr1-40348260-G-A
• rs4660403
• ENST00000435168.6:c.-83+3350G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-40348260-G-A
• chr1-40348260-G-C
• chr1-40348260-G-T

Variant summary

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000435168.6. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMAP2	ENST00000435168.6	TSL:5	c.-83+3350G>A		intron	N/A	ENSP00000389895.2

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

African (AFR) AF: 0.964 AC: 40050 AN: 41548

American (AMR) AF: 0.847 AC: 12942 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.786 AC: 2727 AN: 3470

East Asian (EAS) AF: 0.963 AC: 5004 AN: 5196

South Asian (SAS) AF: 0.886 AC: 4282 AN: 4832

European-Finnish (FIN) AF: 0.754 AC: 7977 AN: 10574

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.799 AC: 54320 AN: 67988

Other (OTH) AF: 0.843 AC: 1777 AN: 2108

Alfa AF: 0.813 Hom.: 28788

Bravo AF: 0.864

Asia WGS AF: 0.932 AC: 3239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.8
DANN	Benign	0.46
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs4660403; hg19: chr1-40813932;