chr1-40417423-C-T

Position:

• chr1-40417423-C-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.88).
• 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/exons	MANE	Protein	UniProt
SMAP2	NM_022733.3	c.1164+327C>T		intron_variant		ENST00000372718.8	NP_073570.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SMAP2	ENST00000372718.8	c.1164+327C>T		intron_variant		1	NM_022733.3	ENSP00000361803.3
SMAP2	ENST00000614549.4	c.1149+327C>T		intron_variant		1		ENSP00000479285.1
SMAP2	ENST00000372708.5	c.1074+327C>T		intron_variant		1		ENSP00000361793.1
SMAP2	ENST00000539317.2	c.924+327C>T		intron_variant		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

Gnomad4 AFR AF: 0.0858

Gnomad4 AMR AF: 0.0859

Gnomad4 ASJ AF: 0.0989

Gnomad4 EAS AF: 0.164

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.0688

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.0829

Alfa AF: 0.0993 Hom.: 127

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2235701; hg19: chr1-40883095;