rs870801

Variant names:

• chr10-70169990-C-A
• rs870801
• NM_020150.5:c.-17+423G>T

Your query was ambiguous. Multiple possible variants found:

• chr10-70169990-C-A
• chr10-70169990-C-G
• chr10-70169990-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020150.5(SAR1A):​c.-17+423G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 151,942 control chromosomes in the GnomAD database, including 11,987 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 0.38 (11987 hom., cov: 31)
• Consequence: SAR1A NM_020150.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.387
• Publications: 13 publications found

Genes affected

SAR1A (HGNC:10534): (secretion associated Ras related GTPase 1A) Predicted to enable GTPase activity. Involved in COPII-coated vesicle cargo loading. Part of COPII vesicle coat. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020150.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAR1A	NM_020150.5	MANE Select	c.-17+423G>T		intron	N/A	NP_064535.1	Q9NR31-1
	SAR1A	NM_001142648.2		c.-87+423G>T		intron	N/A	NP_001136120.1	Q9NR31-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAR1A	ENST00000373241.9	TSL:1 MANE Select	c.-17+423G>T		intron	N/A	ENSP00000362338.4	Q9NR31-1
	SAR1A	ENST00000373242.6	TSL:2	c.-87+423G>T		intron	N/A	ENSP00000362339.1	Q9NR31-1
	SAR1A	ENST00000870136.1		c.-13+423G>T		intron	N/A	ENSP00000540195.1

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57680 AN: 151824 Hom.: 11979 Cov.: 31

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.380 AC: 57695 AN: 151942 Hom.: 11987 Cov.: 31 AF XY: 0.381 AC XY: 28282 AN XY: 74234

African (AFR) AF: 0.204 AC: 8451 AN: 41468

American (AMR) AF: 0.501 AC: 7647 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1458 AN: 3472

East Asian (EAS) AF: 0.559 AC: 2872 AN: 5140

South Asian (SAS) AF: 0.421 AC: 2020 AN: 4802

European-Finnish (FIN) AF: 0.393 AC: 4151 AN: 10560

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.436 AC: 29640 AN: 67912

Other (OTH) AF: 0.400 AC: 843 AN: 2108

Alfa AF: 0.402 Hom.: 6994

Bravo AF: 0.386

Asia WGS AF: 0.474 AC: 1649 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.8
DANN	Benign	0.74
PhyloP100		0.39
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: rs870801; hg19: chr10-71929746;