10-70170313-A-G

Variant names:

• chr10-70170313-A-G
• rs4282891
• NM_020150.5:c.-17+100T>C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_020150.5(SAR1A):​c.-17+100T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.00080 (0 hom., cov: 11)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SAR1A NM_020150.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.167
• Publications: 7 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).

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+100T>C		intron	N/A	NP_064535.1	Q9NR31-1
	SAR1A	NM_001142648.2		c.-87+100T>C		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+100T>C		intron	N/A	ENSP00000362338.4	Q9NR31-1
	SAR1A	ENST00000373242.6	TSL:2	c.-87+100T>C		intron	N/A	ENSP00000362339.1	Q9NR31-1
	SAR1A	ENST00000870136.1		c.-13+100T>C		intron	N/A	ENSP00000540195.1

Frequencies

GnomAD3 genomes AF: 0.000797 AC: 73 AN: 91642 Hom.: 0 Cov.: 11

Gnomad AFR AF: 0.000438

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00229

Gnomad ASJ AF: 0.00116

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00228

Gnomad FIN AF: 0.000400

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000650

Gnomad OTH AF: 0.000829

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

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: 0.000796 AC: 73 AN: 91668 Hom.: 0 Cov.: 11 AF XY: 0.000952 AC XY: 41 AN XY: 43086

African (AFR) AF: 0.000437 AC: 8 AN: 18320

American (AMR) AF: 0.00229 AC: 21 AN: 9184

Ashkenazi Jewish (ASJ) AF: 0.00116 AC: 3 AN: 2576

East Asian (EAS) AF: 0.00 AC: 0 AN: 2690

South Asian (SAS) AF: 0.00229 AC: 6 AN: 2620

European-Finnish (FIN) AF: 0.000400 AC: 2 AN: 4994

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 202

European-Non Finnish (NFE) AF: 0.000650 AC: 32 AN: 49256

Other (OTH) AF: 0.000826 AC: 1 AN: 1210

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	14
DANN	Benign	0.71
PhyloP100		-0.17
PromoterAI		0.14	Neutral

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: rs4282891; hg19: chr10-71930069;