1-40419041-A-T

Position:

• chr1-40419041-A-T

Variant summary

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

The ENST00000372718.8(SMAP2):​c.1164+1945A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.594 in 151,872 control chromosomes in the GnomAD database, including 27,491 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 0.59 (27491 hom., cov: 31)
• Consequence: SMAP2 ENST00000372718.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.714

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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SMAP2	NM_022733.3	c.1164+1945A>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+1945A>T		intron_variant		1	NM_022733.3	ENSP00000361803	P1
SMAP2	ENST00000372708.5	c.1074+1945A>T		intron_variant		1		ENSP00000361793
SMAP2	ENST00000614549.4	c.1149+1945A>T		intron_variant		1		ENSP00000479285
SMAP2	ENST00000539317.2	c.924+1945A>T		intron_variant		2		ENSP00000442835

Frequencies

GnomAD3 genomes AF: 0.594 AC: 90198 AN: 151754 Hom.: 27470 Cov.: 31

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.830

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.723

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.696

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.634

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

GnomAD4 genome AF: 0.594 AC: 90259 AN: 151872 Hom.: 27491 Cov.: 31 AF XY: 0.596 AC XY: 44243 AN XY: 74234

Gnomad4 AFR AF: 0.453

Gnomad4 AMR AF: 0.662

Gnomad4 ASJ AF: 0.723

Gnomad4 EAS AF: 0.674

Gnomad4 SAS AF: 0.697

Gnomad4 FIN AF: 0.594

Gnomad4 NFE AF: 0.640

Gnomad4 OTH AF: 0.638

Alfa AF: 0.405 Hom.: 881

Bravo AF: 0.594

Asia WGS AF: 0.673 AC: 2341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.44
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs446738; hg19: chr1-40884713;