rs2235701

Variant names:

• chr1-40417423-C-T
• rs2235701
• NM_022733.3:c.1164+327C>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.1164+327C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0962 in 152,080 control chromosomes in the GnomAD database, including 745 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 0.096 (745 hom., cov: 30)
• Consequence: SMAP2 NM_022733.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.10
• Publications: 6 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMAP2	NM_022733.3	c.1164+327C>T		intron_variant	Intron 9 of 9	ENST00000372718.8	NP_073570.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMAP2	ENST00000372718.8	c.1164+327C>T		intron_variant	Intron 9 of 9	1	NM_022733.3	ENSP00000361803.3
SMAP2	ENST00000614549.4	c.1149+327C>T		intron_variant	Intron 9 of 9	1		ENSP00000479285.1
SMAP2	ENST00000372708.5	c.1074+327C>T		intron_variant	Intron 9 of 9	1		ENSP00000361793.1
SMAP2	ENST00000539317.2	c.924+327C>T		intron_variant	Intron 9 of 9	2		ENSP00000442835.1

Frequencies

GnomAD3 genomes AF: 0.0963 AC: 14639 AN: 151962 Hom.: 749 Cov.: 30

Gnomad AFR AF: 0.0861

Gnomad AMI AF: 0.0529

Gnomad AMR AF: 0.0856

Gnomad ASJ AF: 0.0989

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.0688

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.0838

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

GnomAD4 genome AF: 0.0962 AC: 14629 AN: 152080 Hom.: 745 Cov.: 30 AF XY: 0.0951 AC XY: 7067 AN XY: 74344

African (AFR) AF: 0.0858 AC: 3558 AN: 41492

American (AMR) AF: 0.0859 AC: 1312 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0989 AC: 343 AN: 3468

East Asian (EAS) AF: 0.164 AC: 846 AN: 5146

South Asian (SAS) AF: 0.128 AC: 618 AN: 4816

European-Finnish (FIN) AF: 0.0688 AC: 728 AN: 10578

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 6983 AN: 67986

Other (OTH) AF: 0.0829 AC: 175 AN: 2110

Alfa AF: 0.103 Hom.: 274

Bravo AF: 0.0922

Asia WGS AF: 0.134 AC: 466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.17
DANN	Benign	0.73
PhyloP100		-2.1
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: rs2235701; hg19: chr1-40883095;