rs4282891

chr10-70170313-A-Cchr10-70170313-A-Gchr10-70170313-A-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+100T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.823 in 91,048 control chromosomes in the GnomAD database, including 29,435 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 0.82 (29435 hom., cov: 11)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: SAR1A NM_020150.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.167

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=-0.56).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.875 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SAR1A	NM_020150.5	c.-17+100T>G		intron_variant		ENST00000373241.9
SAR1A	NM_001142648.2	c.-87+100T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SAR1A	ENST00000373241.9	c.-17+100T>G		intron_variant		1	NM_020150.5	P1
SAR1A	ENST00000373239.2	c.-217+100T>G		intron_variant		3
SAR1A	ENST00000373242.6	c.-87+100T>G		intron_variant		2		P1

Frequencies

GnomAD3 genomes AF: 0.823 AC: 74880 AN: 91024 Hom.: 29437 Cov.: 11

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.892

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.838

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.874

Gnomad NFE AF: 0.882

Gnomad OTH AF: 0.822

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.823 AC: 74891 AN: 91046 Hom.: 29435 Cov.: 11 AF XY: 0.818 AC XY: 34993 AN XY: 42790

Gnomad4 AFR AF: 0.675

Gnomad4 AMR AF: 0.824

Gnomad4 ASJ AF: 0.796

Gnomad4 EAS AF: 0.671

Gnomad4 SAS AF: 0.840

Gnomad4 FIN AF: 0.847

Gnomad4 NFE AF: 0.882

Gnomad4 OTH AF: 0.820

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
Cadd	Benign	14
Dann	Benign	0.71

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: rs4282891; hg19: chr10-71930069;