rs11438971

Variant names:

• chr10-70171117-C-CA
• rs11438971
• ENST00000948610.1:c.-330_-329insT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000948610.1(SAR1A):​c.-330_-329insT 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 0.94 (66588 hom., cov: 0)
• Consequence: SAR1A ENST00000948610.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.691
• Publications: 2 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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 is higher than 0.05.

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.-330_-329insT		upstream_gene	N/A	ENSP00000618669.1

Frequencies

GnomAD3 genomes AF: 0.936 AC: 141981 AN: 151694 Hom.: 66533 Cov.: 0

Gnomad AFR AF: 0.955

Gnomad AMI AF: 0.988

Gnomad AMR AF: 0.943

Gnomad ASJ AF: 0.903

Gnomad EAS AF: 0.991

Gnomad SAS AF: 0.904

Gnomad FIN AF: 0.951

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.920

Gnomad OTH AF: 0.923

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

GnomAD4 genome AF: 0.936 AC: 142095 AN: 151812 Hom.: 66588 Cov.: 0 AF XY: 0.937 AC XY: 69466 AN XY: 74162

African (AFR) AF: 0.955 AC: 39544 AN: 41394

American (AMR) AF: 0.943 AC: 14391 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.903 AC: 3135 AN: 3470

East Asian (EAS) AF: 0.991 AC: 5104 AN: 5152

South Asian (SAS) AF: 0.904 AC: 4336 AN: 4796

European-Finnish (FIN) AF: 0.951 AC: 9989 AN: 10508

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.920 AC: 62495 AN: 67910

Other (OTH) AF: 0.923 AC: 1948 AN: 2110

Alfa AF: 0.929 Hom.: 8006

Bravo AF: 0.935

Asia WGS AF: 0.950 AC: 3305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.69

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11438971;

hg19: chr10-71930873;