10-70170920-CTTTTTTTTTTTT-CTTTTTTTT

Variant names:

• chr10-70170920-CTTTT-C
• rs5785963
• ENST00000948610.1:c.-136_-133delAAAA

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The ENST00000948610.1(SAR1A):​c.-136_-133delAAAA variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.33 (1406 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: SAR1A ENST00000948610.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.46
• 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: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000948610.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAR1A	ENST00000948610.1		c.-136_-133delAAAA		upstream_gene	N/A	ENSP00000618669.1

Frequencies

GnomAD3 genomes AF: 0.328 AC: 23753 AN: 72372 Hom.: 1405 Cov.: 0

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.348

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.328 AC: 23748 AN: 72384 Hom.: 1406 Cov.: 0 AF XY: 0.328 AC XY: 10464 AN XY: 31918

African (AFR) AF: 0.197 AC: 3269 AN: 16552

American (AMR) AF: 0.439 AC: 2413 AN: 5500

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 797 AN: 2326

East Asian (EAS) AF: 0.458 AC: 956 AN: 2088

South Asian (SAS) AF: 0.386 AC: 638 AN: 1654

European-Finnish (FIN) AF: 0.333 AC: 310 AN: 930

Middle Eastern (MID) AF: 0.338 AC: 25 AN: 74

European-Non Finnish (NFE) AF: 0.354 AC: 14783 AN: 41756

Other (OTH) AF: 0.345 AC: 319 AN: 924

Alfa AF: 0.139 Hom.: 236

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.5

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs5785963; hg19: chr10-71930676;