rs10498874

Positions:

• chr6-70747350-A-C

Variant summary

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

The NM_001044305.3(SMAP1):​c.253-7630A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 152,058 control chromosomes in the GnomAD database, including 14,742 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 0.43 (14742 hom., cov: 32)
• Consequence: SMAP1 NM_001044305.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.225

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SMAP1	NM_001044305.3	c.253-7630A>C		intron_variant		ENST00000370455.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SMAP1	ENST00000370455.8	c.253-7630A>C		intron_variant		1	NM_001044305.3	P3
SMAP1	ENST00000316999.9	c.253-7630A>C		intron_variant		1		A1
SMAP1	ENST00000619054.4	c.223-7630A>C		intron_variant		1
SMAP1	ENST00000370452.7	c.253-7630A>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66090 AN: 151940 Hom.: 14743 Cov.: 32

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.435 AC: 66102 AN: 152058 Hom.: 14742 Cov.: 32 AF XY: 0.433 AC XY: 32168 AN XY: 74324

Gnomad4 AFR AF: 0.377

Gnomad4 AMR AF: 0.421

Gnomad4 ASJ AF: 0.403

Gnomad4 EAS AF: 0.232

Gnomad4 SAS AF: 0.497

Gnomad4 FIN AF: 0.445

Gnomad4 NFE AF: 0.483

Gnomad4 OTH AF: 0.457

Alfa AF: 0.469 Hom.: 34335

Bravo AF: 0.425

Asia WGS AF: 0.374 AC: 1301 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.4
DANN	Benign	0.69

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: rs10498874; hg19: chr6-71457053;