rs12415976

Variant names:

• chr10-70154752-C-T
• rs12415976
• NM_020150.5:c.349-783G>A

Variant summary

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

The NM_020150.5(SAR1A):​c.349-783G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.381 in 152,042 control chromosomes in the GnomAD database, including 12,066 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 (12066 hom., cov: 32)
• Consequence: SAR1A NM_020150.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.640

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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SAR1A	NM_020150.5	c.349-783G>A		intron_variant	Intron 5 of 6	ENST00000373241.9	NP_064535.1
SAR1A	NM_001142648.2	c.349-783G>A		intron_variant	Intron 6 of 7		NP_001136120.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SAR1A	ENST00000373241.9	c.349-783G>A		intron_variant	Intron 5 of 6	1	NM_020150.5	ENSP00000362338.4
SAR1A	ENST00000373238.5	c.349-783G>A		intron_variant	Intron 5 of 6	2		ENSP00000362335.1
SAR1A	ENST00000373242.6	c.349-783G>A		intron_variant	Intron 6 of 7	2		ENSP00000362339.1
SAR1A	ENST00000452767.1	c.96+336G>A		intron_variant	Intron 2 of 3	5		ENSP00000398165.1

Frequencies

GnomAD3 genomes AF: 0.381 AC: 57917 AN: 151924 Hom.: 12058 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.381 AC: 57932 AN: 152042 Hom.: 12066 Cov.: 32 AF XY: 0.382 AC XY: 28403 AN XY: 74304

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.502

Gnomad4 ASJ AF: 0.422

Gnomad4 EAS AF: 0.562

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.394

Gnomad4 NFE AF: 0.438

Gnomad4 OTH AF: 0.403

Alfa AF: 0.395 Hom.: 1571

Bravo AF: 0.386

Asia WGS AF: 0.474 AC: 1649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.67
DANN	Benign	0.29

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: rs12415976; hg19: chr10-71914508;