rs781985

chr6-70670231-A-Gchr6-70670231-A-T

Variant summary

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

The NM_001044305.3(SMAP1):c.118+2090A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.459 in 151,978 control chromosomes in the GnomAD database, including 16,337 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 0.46 (16337 hom., cov: 32)
• Consequence: SMAP1 NM_001044305.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.290

Genes affected

SMAP1 (HGNC:19651): (small ArfGAP 1) The protein encoded by this gene is similar to the mouse stromal membrane-associated protein-1. This similarity suggests that this human gene product is also a type II membrane glycoprotein involved in the erythropoietic stimulatory activity of stromal cells. Alternate splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SMAP1	NM_001044305.3	c.118+2090A>G		intron_variant		ENST00000370455.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SMAP1	ENST00000370455.8	c.118+2090A>G		intron_variant		1	NM_001044305.3	P3
SMAP1	ENST00000316999.9	c.118+2090A>G		intron_variant		1		A1
SMAP1	ENST00000619054.4	c.88+1515A>G		intron_variant		1
SMAP1	ENST00000370452.7	c.118+2090A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69783 AN: 151860 Hom.: 16334 Cov.: 32

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.459 AC: 69819 AN: 151978 Hom.: 16337 Cov.: 32 AF XY: 0.457 AC XY: 33907 AN XY: 74252

Gnomad4 AFR AF: 0.464

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.401

Gnomad4 EAS AF: 0.233

Gnomad4 SAS AF: 0.499

Gnomad4 FIN AF: 0.443

Gnomad4 NFE AF: 0.483

Gnomad4 OTH AF: 0.474

Alfa AF: 0.341 Hom.: 880

Bravo AF: 0.453

Asia WGS AF: 0.380 AC: 1320 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	4.7
Dann	Benign	0.54

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs781985; hg19: chr6-71379934; COSMIC: COSV57640523;