chr10-70167429-G-T

Variant names:

• chr10-70167429-G-T
• rs2394641
• NM_020150.5:c.-17+2984C>A

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+2984C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.029 in 152,146 control chromosomes in the GnomAD database, including 89 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 0.029 (89 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SAR1A NM_020150.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131
• Publications: 1 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=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0531 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAR1A	NM_020150.5	MANE Select	c.-17+2984C>A		intron	N/A	NP_064535.1
	SAR1A	NM_001142648.2		c.-87+2984C>A		intron	N/A	NP_001136120.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAR1A	ENST00000373241.9	TSL:1 MANE Select	c.-17+2984C>A		intron	N/A	ENSP00000362338.4
	SAR1A	ENST00000373239.2	TSL:3	c.-120C>A		5_prime_UTR	Exon 2 of 5	ENSP00000362336.2
	SAR1A	ENST00000373242.6	TSL:2	c.-87+2984C>A		intron	N/A	ENSP00000362339.1

Frequencies

GnomAD3 genomes AF: 0.0290 AC: 4408 AN: 152026 Hom.: 89 Cov.: 32

Gnomad AFR AF: 0.00674

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.0162

Gnomad ASJ AF: 0.0159

Gnomad EAS AF: 0.0584

Gnomad SAS AF: 0.0263

Gnomad FIN AF: 0.0492

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0411

Gnomad OTH AF: 0.0197

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0290 AC: 4406 AN: 152146 Hom.: 89 Cov.: 32 AF XY: 0.0281 AC XY: 2090 AN XY: 74384

African (AFR) AF: 0.00672 AC: 279 AN: 41526

American (AMR) AF: 0.0162 AC: 247 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0159 AC: 55 AN: 3470

East Asian (EAS) AF: 0.0586 AC: 303 AN: 5174

South Asian (SAS) AF: 0.0259 AC: 125 AN: 4820

European-Finnish (FIN) AF: 0.0492 AC: 521 AN: 10582

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0411 AC: 2793 AN: 67992

Other (OTH) AF: 0.0204 AC: 43 AN: 2108

Alfa AF: 0.0388 Hom.: 42

Bravo AF: 0.0252

Asia WGS AF: 0.0300 AC: 103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	13
DANN	Benign	0.91
PhyloP100		0.13
Mutation Taster		=100/0	polymorphism

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: rs2394641; hg19: chr10-71927185;