chr10-70170920-CTTTTTTTTT-C

Variant names:

• chr10-70170920-CTTTTTTTTT-C
• rs5785963
• ENST00000948610.1:c.-141_-133delAAAAAAAAA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1 BS2

The ENST00000948610.1(SAR1A):​c.-141_-133delAAAAAAAAA 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 0.011 (10 hom., cov: 0)
• 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: Benign. The variant received -8 ACMG points.

• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0107 (782/73166) while in subpopulation AFR AF = 0.0417 (694/16626). AF 95% confidence interval is 0.0392. There are 10 homozygotes in GnomAd4. There are 384 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 10 gene

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.-141_-133delAAAAAAAAA		upstream_gene	N/A	ENSP00000618669.1

Frequencies

GnomAD3 genomes AF: 0.0107 AC: 782 AN: 73154 Hom.: 10 Cov.: 0

Gnomad AFR AF: 0.0418

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00892

Gnomad ASJ AF: 0.000427

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00120

Gnomad FIN AF: 0.00108

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000588

Gnomad OTH AF: 0.0109

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

GnomAD4 genome AF: 0.0107 AC: 782 AN: 73166 Hom.: 10 Cov.: 0 AF XY: 0.0119 AC XY: 384 AN XY: 32208

African (AFR) AF: 0.0417 AC: 694 AN: 16626

American (AMR) AF: 0.00891 AC: 49 AN: 5502

Ashkenazi Jewish (ASJ) AF: 0.000427 AC: 1 AN: 2340

East Asian (EAS) AF: 0.00 AC: 0 AN: 2058

South Asian (SAS) AF: 0.00121 AC: 2 AN: 1652

European-Finnish (FIN) AF: 0.00108 AC: 1 AN: 928

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 74

European-Non Finnish (NFE) AF: 0.000589 AC: 25 AN: 42480

Other (OTH) AF: 0.0108 AC: 10 AN: 924

Alfa AF: 0.00 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

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

Other links and lift over

dbSNP: rs5785963; hg19: chr10-71930676;