chr6-70670231-A-G

Variant names:

• chr6-70670231-A-G
• rs781985
• NM_001044305.3:c.118+2090A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001044305.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMAP1	NM_001044305.3	MANE Select	c.118+2090A>G		intron	N/A	NP_001037770.1
	SMAP1	NM_001281440.1		c.88+1515A>G		intron	N/A	NP_001268369.1
	SMAP1	NM_021940.5		c.118+2090A>G		intron	N/A	NP_068759.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMAP1	ENST00000370455.8	TSL:1 MANE Select	c.118+2090A>G		intron	N/A	ENSP00000359484.3
	SMAP1	ENST00000619054.4	TSL:1	c.88+1515A>G		intron	N/A	ENSP00000484538.1
	SMAP1	ENST00000316999.9	TSL:1	c.118+2090A>G		intron	N/A	ENSP00000313382.5

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

African (AFR) AF: 0.464 AC: 19246 AN: 41456

American (AMR) AF: 0.428 AC: 6540 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1389 AN: 3464

East Asian (EAS) AF: 0.233 AC: 1204 AN: 5170

South Asian (SAS) AF: 0.499 AC: 2400 AN: 4812

European-Finnish (FIN) AF: 0.443 AC: 4661 AN: 10532

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.483 AC: 32798 AN: 67956

Other (OTH) AF: 0.474 AC: 1001 AN: 2112

Alfa AF: 0.348 Hom.: 964

Bravo AF: 0.453

Asia WGS AF: 0.380 AC: 1320 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.7
DANN	Benign	0.54
PhyloP100		0.29
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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