rs870801

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SAR1A	NM_020150.5	c.-17+423G>T		intron_variant		ENST00000373241.9
SAR1A	NM_001142648.2	c.-87+423G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SAR1A	ENST00000373241.9	c.-17+423G>T		intron_variant		1	NM_020150.5	P1
SAR1A	ENST00000373239.2	c.-217+423G>T		intron_variant		3
SAR1A	ENST00000373242.6	c.-87+423G>T		intron_variant		2		P1

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

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.501

Gnomad4 ASJ AF: 0.420

Gnomad4 EAS AF: 0.559

Gnomad4 SAS AF: 0.421

Gnomad4 FIN AF: 0.393

Gnomad4 NFE AF: 0.436

Gnomad4 OTH AF: 0.400

Alfa AF: 0.401 Hom.: 6238

Bravo AF: 0.386

Asia WGS AF: 0.474 AC: 1649 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.8
DANN	Benign	0.74

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: rs870801; hg19: chr10-71929746;